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OpenMx Installation on Redhat Cluster

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Joined: 04/13/2017 - 11:44
OpenMx Installation on Redhat Cluster

Greeting all,

I am attempting to install OpenMx on a x86_64 Redhat Linux cluster running R 3.3.1. I am installing it using the command source('http://openmx.psyc.virginia.edu/getOpenMx.R').

Based on the errors I am getting it looks as if R is not invoking a compiler. Here is the full output of what I am getting:

> source('http://openmx.psyc.virginia.edu/getOpenMx.R')
You are now installing the latest version of OpenMx.--- Please select a CRAN mirror for use in this session ---
HTTPS CRAN mirror
 
 1: 0-Cloud [https]                 2: Algeria [https]
 3: Australia (Canberra) [https]    4: Australia (Melbourne) [https]
 5: Australia (Perth) [https]       6: Austria [https]
 7: Belgium (Ghent) [https]         8: Brazil (RJ) [https]
 9: Brazil (SP 1) [https]          10: Bulgaria [https]
11: Canada (MB) [https]            12: Chile 1 [https]
13: Chile 2 [https]                14: China (Beijing) [https]
15: China (Hefei) [https]          16: China (Lanzhou) [https]
17: Colombia (Cali) [https]        18: Czech Republic [https]
19: Denmark [https]                20: Estonia [https]
21: France (Lyon 1) [https]        22: France (Lyon 2) [https]
23: France (Marseille) [https]     24: France (Montpellier) [https]
25: France (Paris 2) [https]       26: Germany (Göttingen) [https]
27: Germany (Münster) [https]      28: Iceland [https]
29: India [https]                  30: Indonesia (Jakarta) [https]
31: Ireland [https]                32: Italy (Padua) [https]
33: Japan (Tokyo) [https]          34: Malaysia [https]
35: Mexico (Mexico City) [https]   36: New Zealand [https]
37: Norway [https]                 38: Philippines [https]
39: Russia (Moscow) [https]        40: Serbia [https]
41: Spain (A Coruña) [https]       42: Spain (Madrid) [https]
43: Sweden [https]                 44: Switzerland [https]
45: Taiwan (Chungli) [https]       46: Turkey (Denizli) [https]
47: Turkey (Mersin) [https]        48: UK (Bristol) [https]
49: UK (Cambridge) [https]         50: UK (London 1) [https]
51: USA (CA 1) [https]             52: USA (IA) [https]
53: USA (IN) [https]               54: USA (KS) [https]
55: USA (MI 1) [https]             56: USA (OR) [https]
57: USA (TN) [https]               58: USA (TX 1) [https]
59: USA (TX 2) [https]             60: (HTTP mirrors)
 
 
Selection: 51
also installing the dependency ‘xml2’
 
trying URL 'https://cran.cnr.berkeley.edu/src/contrib/xml2_1.1.1.tar.gz'
Content type 'application/x-gzip' length 244643 bytes (238 KB)
==================================================
downloaded 238 KB
 
trying URL 'https://cran.cnr.berkeley.edu/src/contrib/roxygen2_6.0.1.tar.gz'
Content type 'application/x-gzip' length 150580 bytes (147 KB)
==================================================
downloaded 147 KB
 
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/libxml2
Using PKG_LIBS=-lxml2 -lz -lm
** libs
g++ -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I../inst/include -I/usr/include/libxml2 -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I../inst/include -I/usr/include/libxml2 -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include"   -fpic  -g -O2  -c connection.cpp -o connection.o
g++ -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I../inst/include -I/usr/include/libxml2 -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include"   -fpic  -g -O2  -c xml2_doc.cpp -o xml2_doc.o
xml2_doc.cpp: In function ‘Rcpp::IntegerVector xml_parse_options():
xml2_doc.cpp:82:5: error: ‘XML_PARSE_OLD10’ was not declared in this scope
xml2_doc.cpp:83:5: error: ‘XML_PARSE_NOBASEFIX’ was not declared in this scope
xml2_doc.cpp:84:5: error: ‘XML_PARSE_HUGE’ was not declared in this scope
xml2_doc.cpp:85:5: error: ‘XML_PARSE_OLDSAX’ was not declared in this scope
make: *** [xml2_doc.o] Error 1
ERROR: compilation failed for package ‘xml2’
* removing ‘/exports/apps/R/R-3.3.1/lib64/R/library/xml2’
ERROR: dependency ‘xml2’ is not available for package ‘roxygen2’
* removing ‘/exports/apps/R/R-3.3.1/lib64/R/library/roxygen2’
 
The downloaded source packages are in/tmp/Rtmp7H0wdr/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
trying URL 'http://openmx.psyc.virginia.edu/OpenMx2/src/contrib/OpenMx_2.7.10.tar.gz'
Content type 'application/x-gzip' length 4739360 bytes (4.5 MB)
==================================================
downloaded 4.5 MB
 
* installing *source* package ‘OpenMx’ ...
NOTE: ./configure is not an autoconf generated script.
Change default C/C++ compiler and default compile flags by editing ~/.R/Makevars
** libs
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c Compute.cpp -o Compute.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [Compute.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c ComputeGD.cpp -o ComputeGD.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [ComputeGD.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c ComputeNM.cpp -o ComputeNM.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [ComputeNM.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c ComputeNR.cpp -o ComputeNR.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [ComputeNR.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c ComputeSD.cpp -o ComputeSD.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [ComputeSD.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c FellnerFitFunction.cpp -o FellnerFitFunction.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [FellnerFitFunction.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c MarkovExpectation.cpp -o MarkovExpectation.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [MarkovExpectation.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c MarkovFF.cpp -o MarkovFF.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [MarkovFF.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c ba81quad.cpp -o ba81quad.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [ba81quad.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c dmvnorm.cpp -o dmvnorm.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [dmvnorm.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c fitMultigroup.cpp -o fitMultigroup.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [fitMultigroup.o] Error 127 (ignored)
gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"   -fpic  -g -O2  -c general.c -o general.o
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c glue.cpp -o glue.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [glue.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c matrix.cpp -o matrix.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [matrix.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c merge.cpp -o merge.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [merge.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c nanotimer.cpp -o nanotimer.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [nanotimer.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c nloptcpp.cpp -o nloptcpp.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [nloptcpp.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxAlgebra.cpp -o omxAlgebra.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxAlgebra.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxAlgebraFitFunction.cpp -o omxAlgebraFitFunction.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxAlgebraFitFunction.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxData.cpp -o omxData.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxData.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxExpectation.cpp -o omxExpectation.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxExpectation.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxExpectationBA81.cpp -o omxExpectationBA81.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxExpectationBA81.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxExportBackendState.cpp -o omxExportBackendState.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxExportBackendState.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxFIMLFitFunction.cpp -o omxFIMLFitFunction.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxFIMLFitFunction.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxFIMLSingleIteration.cpp -o omxFIMLSingleIteration.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxFIMLSingleIteration.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxFitFunction.cpp -o omxFitFunction.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxFitFunction.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxFitFunctionBA81.cpp -o omxFitFunctionBA81.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxFitFunctionBA81.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxGREMLExpectation.cpp -o omxGREMLExpectation.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxGREMLExpectation.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxGREMLfitfunction.cpp -o omxGREMLfitfunction.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxGREMLfitfunction.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxHessianCalculation.cpp -o omxHessianCalculation.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxHessianCalculation.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxImportFrontendState.cpp -o omxImportFrontendState.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxImportFrontendState.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxLISRELExpectation.cpp -o omxLISRELExpectation.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxLISRELExpectation.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxMLFitFunction.cpp -o omxMLFitFunction.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxMLFitFunction.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxMatrix.cpp -o omxMatrix.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxMatrix.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxNPSOLSpecific.cpp -o omxNPSOLSpecific.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxNPSOLSpecific.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxNormalExpectation.cpp -o omxNormalExpectation.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxNormalExpectation.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxRAMExpectation.cpp -o omxRAMExpectation.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxRAMExpectation.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxRFitFunction.cpp -o omxRFitFunction.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxRFitFunction.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxRowFitFunction.cpp -o omxRowFitFunction.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxRowFitFunction.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxState.cpp -o omxState.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxState.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxStateSpaceExpectation.cpp -o omxStateSpaceExpectation.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxStateSpaceExpectation.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxSymbolTable.cpp -o omxSymbolTable.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxSymbolTable.o] Error 127 (ignored)
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c omxWLSFitFunction.cpp -o omxWLSFitFunction.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [omxWLSFitFunction.o] Error 127 (ignored)
gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"   -fpic  -g -O2  -c optimize.c -o optimize.o
gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"   -fpic  -g -O2  -c options.c -o options.o
gfortran   -fpic  -g -O2  -c sadmvn.f -o sadmvn.o
gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"   -fpic  -g -O2  -c slsqp.c -o slsqp.o
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c ssMLFit.cpp -o ssMLFit.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [ssMLFit.o] Error 127 (ignored)
gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"   -fpic  -g -O2  -c stop.c -o stop.o
I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c subnp.cpp -o subnp.o
/bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory
make: [subnp.o] Error 127 (ignored)
-shared -L/exports/apps/libs/lib -o OpenMx.so Compute.o ComputeGD.o ComputeNM.o ComputeNR.o ComputeSD.o FellnerFitFunction.o MarkovExpectation.o MarkovFF.o ba81quad.o dmvnorm.o fitMultigroup.o general.o glue.o matrix.o merge.o nanotimer.o nloptcpp.o omxAlgebra.o omxAlgebraFitFunction.o omxData.o omxExpectation.o omxExpectationBA81.o omxExportBackendState.o omxFIMLFitFunction.o omxFIMLSingleIteration.o omxFitFunction.o omxFitFunctionBA81.o omxGREMLExpectation.o omxGREMLfitfunction.o omxHessianCalculation.o omxImportFrontendState.o omxLISRELExpectation.o omxMLFitFunction.o omxMatrix.o omxNPSOLSpecific.o omxNormalExpectation.o omxRAMExpectation.o omxRFitFunction.o omxRowFitFunction.o omxState.o omxStateSpaceExpectation.o omxSymbolTable.o omxWLSFitFunction.o optimize.o options.o sadmvn.o slsqp.o ssMLFit.o stop.o subnp.o -fopenmp -lgfortran -lm -L/exports/apps/R/R-3.3.1/lib64/R/lib -lRblas -L/exports/apps/R/R-3.3.1/lib64/R/lib -lRlapack -L../src -lnpsol -lgfortran -lm
/bin/sh: line 2: -shared: command not found
make: *** [OpenMx.so] Error 127
ERROR: compilation failed for package ‘OpenMx’
* removing ‘/exports/apps/R/R-3.3.1/lib64/R/library/OpenMx’
 
The downloaded source packages are in/tmp/Rtmp7H0wdr/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkg) :
  installation of package ‘xml2’ had non-zero exit status
2: In install.packages(pkg) :
  installation of package ‘roxygen2’ had non-zero exit status
3: In install.packages(pkgs = c("OpenMx"), contriburl = contrib.url(repos,  :
  installation of package ‘OpenMx’ had non-zero exit status

I tried adding a .R/Makevars file in order to force it to use a compiler, but got the roughly the same output. The only difference is that when it did invoke a compiler it invoked the compiler I specified in the Makevars file (mpicc or mpic++) instead of the generic gnu compiler. Here is a copy of my Makevars file:

C=mpicc
CFLAGS=-O3 -ffast-math -fopenmp
CXX=mpic++
FC=mpif90
FCFLAGS=-O3 -ffast-math -fopenmp

Thanks in advance for any help you can give me!
Shane

P.s. I am running OpenMpi 1.4.2

AdminJosh's picture
Offline
Joined: 12/12/2012 - 12:15
CXX1X CXX11

Try setting CXX1X in addition to CXX. I'm not sure if mpic++ can build the OpenMx source code, but it's worth a try.

Shesprich's picture
Offline
Joined: 04/13/2017 - 11:44
CXX1X

So I think that helped. However, I got a new error.

> source('http://openmx.psyc.virginia.edu/getOpenMx.R')
You are now installing the latest version of OpenMx.--- Please select a CRAN mirror for use in this session ---
HTTPS CRAN mirror
 
 1: 0-Cloud [https]                 2: Algeria [https]
 3: Australia (Canberra) [https]    4: Australia (Melbourne) [https]
 5: Australia (Perth) [https]       6: Austria [https]
 7: Belgium (Ghent) [https]         8: Brazil (RJ) [https]
 9: Brazil (SP 1) [https]          10: Bulgaria [https]
11: Canada (MB) [https]            12: Chile 1 [https]
13: Chile 2 [https]                14: China (Beijing) [https]
15: China (Hefei) [https]          16: China (Lanzhou) [https]
17: Colombia (Cali) [https]        18: Czech Republic [https]
19: Denmark [https]                20: Estonia [https]
21: France (Lyon 1) [https]        22: France (Lyon 2) [https]
23: France (Marseille) [https]     24: France (Montpellier) [https]
25: France (Paris 2) [https]       26: Germany (Göttingen) [https]
27: Germany (Münster) [https]      28: Iceland [https]
29: India [https]                  30: Indonesia (Jakarta) [https]
31: Ireland [https]                32: Italy (Padua) [https]
33: Japan (Tokyo) [https]          34: Malaysia [https]
35: Mexico (Mexico City) [https]   36: New Zealand [https]
37: Norway [https]                 38: Philippines [https]
39: Russia (Moscow) [https]        40: Serbia [https]
41: Spain (A Coruña) [https]       42: Spain (Madrid) [https]
43: Sweden [https]                 44: Switzerland [https]
45: Taiwan (Chungli) [https]       46: Turkey (Denizli) [https]
47: Turkey (Mersin) [https]        48: UK (Bristol) [https]
49: UK (Cambridge) [https]         50: UK (London 1) [https]
51: USA (CA 1) [https]             52: USA (IA) [https]
53: USA (IN) [https]               54: USA (KS) [https]
55: USA (MI 1) [https]             56: USA (OR) [https]
57: USA (TN) [https]               58: USA (TX 1) [https]
59: USA (TX 2) [https]             60: (HTTP mirrors)
 
 
Selection: 51
also installing the dependency ‘xml2’
 
trying URL 'https://cran.cnr.berkeley.edu/src/contrib/xml2_1.1.1.tar.gz'
Content type 'application/x-gzip' length 244643 bytes (238 KB)
==================================================
downloaded 238 KB
 
trying URL 'https://cran.cnr.berkeley.edu/src/contrib/roxygen2_6.0.1.tar.gz'
Content type 'application/x-gzip' length 150580 bytes (147 KB)
==================================================
downloaded 147 KB
 
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/libxml2
Using PKG_LIBS=-lxml2 -lz -lm
** libs
mpic++ -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I../inst/include -I/usr/include/libxml2 -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
mpic++ -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I../inst/include -I/usr/include/libxml2 -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include"   -fpic  -g -O2  -c connection.cpp -o connection.o
mpic++ -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I../inst/include -I/usr/include/libxml2 -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include"   -fpic  -g -O2  -c xml2_doc.cpp -o xml2_doc.o
xml2_doc.cpp: In function ‘Rcpp::IntegerVector xml_parse_options():
xml2_doc.cpp:82:5: error: ‘XML_PARSE_OLD10’ was not declared in this scope
xml2_doc.cpp:83:5: error: ‘XML_PARSE_NOBASEFIX’ was not declared in this scope
xml2_doc.cpp:84:5: error: ‘XML_PARSE_HUGE’ was not declared in this scope
xml2_doc.cpp:85:5: error: ‘XML_PARSE_OLDSAX’ was not declared in this scope
make: *** [xml2_doc.o] Error 1
ERROR: compilation failed for package ‘xml2’
* removing ‘/exports/apps/R/R-3.3.1/lib64/R/library/xml2’
ERROR: dependency ‘xml2’ is not available for package ‘roxygen2’
* removing ‘/exports/apps/R/R-3.3.1/lib64/R/library/roxygen2’
 
The downloaded source packages are in/tmp/RtmpQyUo00/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
trying URL 'http://openmx.psyc.virginia.edu/OpenMx2/src/contrib/OpenMx_2.7.10.tar.gz'
Content type 'application/x-gzip' length 4739360 bytes (4.5 MB)
==================================================
downloaded 4.5 MB
 
* installing *source* package ‘OpenMx’ ...
NOTE: ./configure is not an autoconf generated script.
Change default C/C++ compiler and default compile flags by editing ~/.R/Makevars
** libs
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function       -c Compute.cpp -o Compute.o
Compute.cpp: In member function ‘std::string FitContext::getIterationError():
Compute.cpp:898:4: warning: ‘auto’ changes meaning in C++11; please remove it [-Wc++0x-compat]
Compute.cpp:898:10: error: ISO C++ forbids declaration of ‘strwith no type [-fpermissive]
Compute.cpp:898:31: error: invalid initialization of reference of type ‘int&’ from expression of type ‘std::string {aka std::basic_string<char>}’
Compute.cpp:899:13: error: request for member ‘size’ instr’, which is of non-class type ‘int’
Compute.cpp:900:55: error: request for member ‘c_str’ instr’, which is of non-class type ‘int’
make: *** [Compute.o] Error 1
ERROR: compilation failed for package ‘OpenMx’
* removing ‘/exports/apps/R/R-3.3.1/lib64/R/library/OpenMx’
 
The downloaded source packages are in/tmp/RtmpQyUo00/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkg) :
  installation of package ‘xml2’ had non-zero exit status
2: In install.packages(pkg) :
  installation of package ‘roxygen2’ had non-zero exit status
3: In install.packages(pkgs = c("OpenMx"), contriburl = contrib.url(repos,  :
  installation of package ‘OpenMx’ had non-zero exit status

Also you mentioned that mpic++ won't compile the OpenMx source code. However, if I want to run it with OpenMPI then what do I compile it with?

Thanks,
Shane

AdminJosh's picture
Offline
Joined: 12/12/2012 - 12:15
mpic++

Like many R extensions, OpenMx requires C++11. What is mpic++ ? Is it based on gcc? Which version?

Shesprich's picture
Offline
Joined: 04/13/2017 - 11:44
mpic++

mpic++ is just a wrapper for g++ which allows for parallel computing. I am using gcc version 4.7 as my back end compiler. According to https://gcc.gnu.org/gcc-4.7/cxx0x_status.html it looks like gcc/4.7 may not have full c++11 support. I will look into upgrading my version of gcc and get back to you. Thanks for your help so far!

Shane

AdminJosh's picture
Offline
Joined: 12/12/2012 - 12:15
gcc version

Ah, OK. You need at least gcc version 4.9.

Shesprich's picture
Offline
Joined: 04/13/2017 - 11:44
OpenMx Compiled but won't run properly

Thanks for all your help so far. I installed gcc/4.9.3 updated my Makevars file and despite one small error (shown in log below) got OpenMx to compile. However, I tried running a simple model

require(OpenMx)
data(demoOneFactor)
factorModel <- mxModel("One Factor",
      mxMatrix("Full", 5, 1, values=0.8,
           free=TRUE, name="A"),
      mxMatrix("Symm", 1, 1, values=1,
           free=FALSE, name="L"),
      mxMatrix("Diag", 5, 5, values=1,
           free=TRUE, name="U"),
      mxAlgebra(A %*% L %*% t(A) + U, name="R"),
      mxExpectationNormal(covariance = "R",
            dimnames = names(demoOneFactor)),
      mxFitFunctionML(),
      mxData(cov(demoOneFactor), type="cov", numObs=500))
factorModelFit <- mxRun(factorModel)

and got the following error

Running One Factor with 10 parameters
Warning message:
In model 'One Factor' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED)

I tried that same model on my laptop (which is more up to date, but only has 4 cores) and it works perfectly, so I am assuming that it is still and issue with the compilation. Any ideas on what went wrong?

As always thanks for your continuing support. Much obliged,
Shane

P.S here is the output from the "successful" compilation

> source('http://openmx.psyc.virginia.edu/getOpenMx.R')
You are now installing the latest version of OpenMx.trying URL 'http://openmx.psyc.virginia.edu/OpenMx2/src/contrib/OpenMx_2.7.11.tar.gz'
Content type 'application/x-gzip' length 4754607 bytes (4.5 MB)
==================================================
downloaded 4.5 MB
 
* installing *source* package ‘OpenMx’ ...
NOTE: ./configure is not an autoconf generated script.
Change default C/C++ compiler and default compile flags by editing ~/.R/Makevars
** libs
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c Compute.cpp -o Compute.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c ComputeGD.cpp -o ComputeGD.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c ComputeNM.cpp -o ComputeNM.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c ComputeNR.cpp -o ComputeNR.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c ComputeSD.cpp -o ComputeSD.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c FellnerFitFunction.cpp -o FellnerFitFunction.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c MarkovExpectation.cpp -o MarkovExpectation.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c MarkovFF.cpp -o MarkovFF.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c ba81quad.cpp -o ba81quad.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c dmvnorm.cpp -o dmvnorm.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c fitMultigroup.cpp -o fitMultigroup.o
gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"   -fpic  -O3 -ffast-math -fopenmp -std=c++11 -fpic -c general.c -o general.o
cc1: warning: command line option ‘-std=c++11is valid for C++/ObjC++ but not for C
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c glue.cpp -o glue.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c matrix.cpp -o matrix.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c merge.cpp -o merge.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c nanotimer.cpp -o nanotimer.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c nloptcpp.cpp -o nloptcpp.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxAlgebra.cpp -o omxAlgebra.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxAlgebraFitFunction.cpp -o omxAlgebraFitFunction.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxData.cpp -o omxData.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxExpectation.cpp -o omxExpectation.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxExpectationBA81.cpp -o omxExpectationBA81.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxExportBackendState.cpp -o omxExportBackendState.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxFIMLFitFunction.cpp -o omxFIMLFitFunction.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxFIMLSingleIteration.cpp -o omxFIMLSingleIteration.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxFitFunction.cpp -o omxFitFunction.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxFitFunctionBA81.cpp -o omxFitFunctionBA81.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxGREMLExpectation.cpp -o omxGREMLExpectation.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxGREMLfitfunction.cpp -o omxGREMLfitfunction.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxHessianCalculation.cpp -o omxHessianCalculation.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxImportFrontendState.cpp -o omxImportFrontendState.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxLISRELExpectation.cpp -o omxLISRELExpectation.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxMLFitFunction.cpp -o omxMLFitFunction.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxMatrix.cpp -o omxMatrix.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxNPSOLSpecific.cpp -o omxNPSOLSpecific.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxNormalExpectation.cpp -o omxNormalExpectation.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxRAMExpectation.cpp -o omxRAMExpectation.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxRFitFunction.cpp -o omxRFitFunction.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxRowFitFunction.cpp -o omxRowFitFunction.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxState.cpp -o omxState.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxStateSpaceExpectation.cpp -o omxStateSpaceExpectation.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxSymbolTable.cpp -o omxSymbolTable.o
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxWLSFitFunction.cpp -o omxWLSFitFunction.o
gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"   -fpic  -O3 -ffast-math -fopenmp -std=c++11 -fpic -c optimize.c -o optimize.o
cc1: warning: command line option ‘-std=c++11is valid for C++/ObjC++ but not for C
gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"   -fpic  -O3 -ffast-math -fopenmp -std=c++11 -fpic -c options.c -o options.o
cc1: warning: command line option ‘-std=c++11is valid for C++/ObjC++ but not for C
gfortran   -fpic  -g -O2  -c sadmvn.f -o sadmvn.o
gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"   -fpic  -O3 -ffast-math -fopenmp -std=c++11 -fpic -c slsqp.c -o slsqp.o
cc1: warning: command line option ‘-std=c++11is valid for C++/ObjC++ but not for C
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c ssMLFit.cpp -o ssMLFit.o
gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"   -fpic  -O3 -ffast-math -fopenmp -std=c++11 -fpic -c stop.c -o stop.o
cc1: warning: command line option ‘-std=c++11is valid for C++/ObjC++ but not for C
mpic++  -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG  -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include"  -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c subnp.cpp -o subnp.o
mpic++ -shared -L/exports/apps/libs/lib -o OpenMx.so Compute.o ComputeGD.o ComputeNM.o ComputeNR.o ComputeSD.o FellnerFitFunction.o MarkovExpectation.o MarkovFF.o ba81quad.o dmvnorm.o fitMultigroup.o general.o glue.o matrix.o merge.o nanotimer.o nloptcpp.o omxAlgebra.o omxAlgebraFitFunction.o omxData.o omxExpectation.o omxExpectationBA81.o omxExportBackendState.o omxFIMLFitFunction.o omxFIMLSingleIteration.o omxFitFunction.o omxFitFunctionBA81.o omxGREMLExpectation.o omxGREMLfitfunction.o omxHessianCalculation.o omxImportFrontendState.o omxLISRELExpectation.o omxMLFitFunction.o omxMatrix.o omxNPSOLSpecific.o omxNormalExpectation.o omxRAMExpectation.o omxRFitFunction.o omxRowFitFunction.o omxState.o omxStateSpaceExpectation.o omxSymbolTable.o omxWLSFitFunction.o optimize.o options.o sadmvn.o slsqp.o ssMLFit.o stop.o subnp.o -fopenmp -lgfortran -lm -L/exports/apps/R/R-3.3.1/lib64/R/lib -lRblas -L/exports/apps/R/R-3.3.1/lib64/R/lib -lRlapack -L../src -lnpsol -lgfortran -lm
mkdir -p ../inst/debug
cp *.gcno ../inst/debug/
cp: cannot stat `*.gcno': No such file or directory
make: [save-gcno] Error 1 (ignored)
installing to /exports/apps/R/R-3.3.1/lib64/R/library/OpenMx/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘OpenMx’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘OpenMx’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘OpenMx’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (OpenMx)
 
The downloaded source packages are in
        ‘/tmp/RtmpqI1NIt/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
AdminRobK's picture
Offline
Joined: 01/24/2014 - 12:15
warning, not error; compilation probably OK
However, I tried running a simple model

require(OpenMx)
data(demoOneFactor)
factorModel <- mxModel("One Factor",
      mxMatrix("Full", 5, 1, values=0.8,
           free=TRUE, name="A"),
      mxMatrix("Symm", 1, 1, values=1,
           free=FALSE, name="L"),
      mxMatrix("Diag", 5, 5, values=1,
           free=TRUE, name="U"),
      mxAlgebra(A %*% L %*% t(A) + U, name="R"),
      mxExpectationNormal(covariance = "R",
            dimnames = names(demoOneFactor)),
      mxFitFunctionML(),
      mxData(cov(demoOneFactor), type="cov", numObs=500))
factorModelFit <- mxRun(factorModel)

and got the following error

Running One Factor with 10 parameters
Warning message:
In model 'One Factor' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED)

I tried that same model on my laptop (which is more up to date, but only has 4 cores) and it works perfectly, so I am assuming that it is still and issue with the compilation. Any ideas on what went wrong?

The message you're seeing is a warning, not an error; if it were an error, it would have been fatal to mxRun(), which would not have returned a value. The warning you're seeing concerns the quality of OpenMx's obtained solution, and is not even that uncommon. In this particular case, I strongly suspect the warning is spurious. Since the release of v2.7.11, we've changed OpenMx's criterion for an "acceptable" unconstrained solution to something more reasonable, so spurious warnings of this sort should be less common in future releases.

So, I doubt it's a sign that something went wrong while compiling. I admit I'm a bit surprised that you ran the same model on a different system and got no warning. Were both systems running OpenMx v2.7.11, and on the same platform (try mxVersion())? Also, are the solutions substantially equivalent (use summary(factorModelFit))?

Shesprich's picture
Offline
Joined: 04/13/2017 - 11:44
Outputs

Here are the outputs from both runs

laptop:

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
 
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
 
  Natural language support but running in an English locale
 
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
 
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
 
> require(OpenMx)
Loading required package: OpenMx
To take full advantage of multiple cores, use:
  mxOption(NULL, 'Number of Threads', parallel::detectCores())
> data(demoOneFactor)
> factorModel <- mxModel("One Factor",
+       mxMatrix("Full", 5, 1, values=0.8,
+            free=TRUE, name="A"),
+       mxMatrix("Symm", 1, 1, values=1,
+            free=FALSE, name="L"),
+       mxMatrix("Diag", 5, 5, values=1,
+            free=TRUE, name="U"),
+       mxAlgebra(A %*% L %*% t(A) + U, name="R"),
+       mxExpectationNormal(covariance = "R",
+             dimnames = names(demoOneFactor)),
+       mxFitFunctionML(),
+       mxData(cov(demoOneFactor), type="cov", numObs=500))
> factorModelFit <- mxRun(factorModel)
Running One Factor with 10 parameters
> summary(factorModelFit)
Summary of One Factor 
 
free parameters:
                name matrix row col   Estimate   Std.Error A
1  One Factor.A[1,1]      A   1   1 0.39675442 0.015518623  
2  One Factor.A[2,1]      A   2   1 0.50315690 0.018196001  
3  One Factor.A[3,1]      A   3   1 0.57666351 0.020407447  
4  One Factor.A[4,1]      A   4   1 0.70207009 0.023963327  
5  One Factor.A[5,1]      A   5   1 0.79545281 0.026616042  
6  One Factor.U[1,1]      U   1   1 0.04073255 0.002804281  
7  One Factor.U[2,2]      U   2   2 0.03794394 0.002797378  
8  One Factor.U[3,3]      U   3   3 0.04074551 0.003142855  
9  One Factor.U[4,4]      U   4   4 0.03930827 0.003398652  
10 One Factor.U[5,5]      U   5   5 0.03621453 0.003667530  
 
Model Statistics: 
               |  Parameters  |  Degrees of Freedom  |  Fit (-2lnL units)
       Model:             10                      5            -3660.5967
   Saturated:             15                      0            -3667.9905
Independence:              5                     10               64.5342
Number of observations/statistics: 500/15
 
chi-square:  χ² ( df=5 ) = 7.393793,  p = 0.1929616
Information Criteria: 
      |  df Penalty  |  Parameters Penalty  |  Sample-Size Adjusted
AIC:      -2.606207               27.39379                       NA
BIC:     -23.679247               69.53987                 37.79926
CFI: 0.9993569 
TLI: 0.9987139   (also known as NNFI) 
RMSEA:  0.03094378  [95% CI (0, 0.08143354)]
Prob(RMSEA <= 0.05): 0.7135768
timestamp: 2017-05-23 13:48:03 
Wall clock time (HH:MM:SS.hh): 00:00:01.26 
optimizer:  CSOLNP 
OpenMx version number: 2.7.11 
Need help?  See help(mxSummary) 
 
> 

Server

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
 
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
 
  Natural language support but running in an English locale
 
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
 
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
 
> require(OpenMx)
Loading required package: OpenMx
To take full advantage of multiple cores, use:
  mxOption(NULL, 'Number of Threads', parallel::detectCores())
> data(demoOneFactor)
> factorModel <- mxModel("One Factor",
+       mxMatrix("Full", 5, 1, values=0.8,
+            free=TRUE, name="A"),
+       mxMatrix("Symm", 1, 1, values=1,
+            free=FALSE, name="L"),
+       mxMatrix("Diag", 5, 5, values=1,
+            free=TRUE, name="U"),
+       mxAlgebra(A %*% L %*% t(A) + U, name="R"),
+       mxExpectationNormal(covariance = "R",
+             dimnames = names(demoOneFactor)),
+       mxFitFunctionML(),
+       mxData(cov(demoOneFactor), type="cov", numObs=500))
> factorModelFit <- mxRun(factorModel)
Running One Factor with 10 parameters
Warning message:
In model 'One Factor' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED) 
> summary(factorModelFit)
Summary of One Factor 
 
The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED) 
 
free parameters:
                name matrix row col Estimate
1  One Factor.A[1,1]      A   1   1       NA
2  One Factor.A[2,1]      A   2   1       NA
3  One Factor.A[3,1]      A   3   1       NA
4  One Factor.A[4,1]      A   4   1       NA
5  One Factor.A[5,1]      A   5   1       NA
6  One Factor.U[1,1]      U   1   1       NA
7  One Factor.U[2,2]      U   2   2       NA
8  One Factor.U[3,3]      U   3   3       NA
9  One Factor.U[4,4]      U   4   4       NA
10 One Factor.U[5,5]      U   5   5       NA
 
Model Statistics: 
               |  Parameters  |  Degrees of Freedom  |  Fit (-2lnL units)
       Model:             10                      5                    NA
   Saturated:             15                      0            -3667.9905
Independence:              5                     10               64.5342
Number of observations/statistics: 500/15
 
Information Criteria: 
      |  df Penalty  |  Parameters Penalty  |  Sample-Size Adjusted
AIC:             NA                     NA                       NA
BIC:             NA                     NA                       NA
To get additional fit indices, see help(mxRefModels)
timestamp: 2017-05-23 13:50:38 
Wall clock time (HH:MM:SS.hh): 00:00:00.62 
optimizer:  CSOLNP 
OpenMx version number: 2.7.11 
Need help?  See help(mxSummary) 
 
> 

Thanks,
Shane

AdminRobK's picture
Offline
Joined: 01/24/2014 - 12:15
maybe there IS a compilation problem
free parameters:
                name matrix row col Estimate
1  One Factor.A[1,1]      A   1   1       NA
2  One Factor.A[2,1]      A   2   1       NA
3  One Factor.A[3,1]      A   3   1       NA
4  One Factor.A[4,1]      A   4   1       NA
5  One Factor.A[5,1]      A   5   1       NA
6  One Factor.U[1,1]      U   1   1       NA
7  One Factor.U[2,2]      U   2   2       NA
8  One Factor.U[3,3]      U   3   3       NA
9  One Factor.U[4,4]      U   4   4       NA
10 One Factor.U[5,5]      U   5   5       NA

Hmm, OK, there definitely seems to be something wrong here.

AdminNeale's picture
Offline
Joined: 03/01/2013 - 14:09
Parallel?

I was wondering if the choices that mpic++ is making re: compiler flags are somehow breaking the build. What do

mpic++ -showme
mpicc -showme:compile
mpicc -showme:link

return?

A higher version of the gnu compiler than 4.9 should also work (might even fix the problem) and could further improve performance.

Shesprich's picture
Offline
Joined: 04/13/2017 - 11:44
Here is the answer to your questions
mpic++ - showme
g++ -I/usr/mpi/gcc/openmpi-1.4.2/include -pthread -L/usr/mpi/gcc/openmpi-1.4.2/lib64 -lmpi_cxx -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
 
mpicc -showme:compile
-I/usr/mpi/gcc/openmpi-1.4.2/include -pthread
 
mpicc -showme:link
-pthread -L/usr/mpi/gcc/openmpi-1.4.2/lib64 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl

Just as a sidebar, I feel like I am getting a slight hint that this module is not often compiled using mpi. Does this module not work well in parallel? Is it not used in parallel often? I am installing this program on a cluster on behalf of a researcher, so I am not very familiar with it myself. I know R can can be, and is used, for parallel computing tasks all the time, but I am unsure if OpenMx is. If this is the case I let the professor know that and we can compile it without mpi. Then he can do his normal R work in parallel and the OpenMx work can be done on a single core.

Thanks for all your help,
Shane

jpritikin's picture
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Joined: 05/24/2012 - 00:35
still broken?

Can we have an update? Are things still broken? If all the estimates are coming out NA, perhaps you could turn on checkpointing. Use mxRun(..., checkpoint=TRUE). This will create a model.omx file in the current directory that might be helpful to diagnose what is going wrong.

Shesprich's picture
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Joined: 04/13/2017 - 11:44
Mx in Parallel/still broken?

So I was waiting for a response to my questions about whether or not Mx is often used in Parallel. I had questions since AdminNeale posted a response with the title "Parallel?" as well as AdminJosh asking the question "What is mpic++ ? Is it based on gcc?" These things made me wonder if it was not common practice to compile in parallel, or if it was even possible. I wanted to make sure I was not wasting my time attempting to compile with OpenMpi. Additionally, I never got a response about whether or not my outputs to mpic++ -showme, mpicc -showme:compile  and mpicc -showme:link were acceptable or if there was something wrong with them. Finally here is an output from the sample simulation using checkpoint=TRUE

cat test.Rout
 
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
 
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
 
  Natural language support but running in an English locale
 
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
 
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
 
> require(OpenMx)
Loading required package: OpenMx
To take full advantage of multiple cores, use:
  mxOption(NULL, 'Number of Threads', parallel::detectCores())
> data(demoOneFactor)
> factorModel <- mxModel("One Factor",
+       mxMatrix("Full", 5, 1, values=0.8,
+            free=TRUE, name="A"),
+       mxMatrix("Symm", 1, 1, values=1,
+            free=FALSE, name="L"),
+       mxMatrix("Diag", 5, 5, values=1,
+            free=TRUE, name="U"),
+       mxAlgebra(A %*% L %*% t(A) + U, name="R"),
+       mxExpectationNormal(covariance = "R",
+             dimnames = names(demoOneFactor)),
+       mxFitFunctionML(),
+       mxData(cov(demoOneFactor), type="cov", numObs=500))
> factorModelFit <- mxRun(factorModel, checkpoint=TRUE)
Running One Factor with 10 parameters
Warning message:
In model 'One Factor' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED)
> summary(factorModelFit)
Summary of One Factor
 
The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED)
 
free parameters:
                name matrix row col Estimate
1  One Factor.A[1,1]      A   1   1       NA
2  One Factor.A[2,1]      A   2   1       NA
3  One Factor.A[3,1]      A   3   1       NA
4  One Factor.A[4,1]      A   4   1       NA
5  One Factor.A[5,1]      A   5   1       NA
6  One Factor.U[1,1]      U   1   1       NA
7  One Factor.U[2,2]      U   2   2       NA
8  One Factor.U[3,3]      U   3   3       NA
9  One Factor.U[4,4]      U   4   4       NA
10 One Factor.U[5,5]      U   5   5       NA
 
Model Statistics:
               |  Parameters  |  Degrees of Freedom  |  Fit (-2lnL units)
       Model:             10                      5                    NA
   Saturated:             15                      0            -3667.9905
Independence:              5                     10               64.5342
Number of observations/statistics: 500/15
 
Information Criteria:
      |  df Penalty  |  Parameters Penalty  |  Sample-Size Adjusted
AIC:             NA                     NA                       NA
BIC:             NA                     NA                       NA
To get additional fit indices, see help(mxRefModels)
timestamp: 2017-06-06 10:52:02
Wall clock time (HH:MM:SS.hh): 00:00:01.30
optimizer:  CSOLNP
OpenMx version number: 2.7.11
Need help?  See help(mxSummary)
 
>
> proc.time()
   user  system elapsed
  4.009   0.282  10.992

I am truly at a loss as to what to try next. Any suggestions would be great, and please let me know if I should continue attempting to compile in parallel or if that is just a waste of time.

Thanks,
Shane

jpritikin's picture
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Joined: 05/24/2012 - 00:35
checkpoint

Can you attach the checkpoint output? It should be in a file named "One Factor.omx" in the current directory.

AdminRobK's picture
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Joined: 01/24/2014 - 12:15
parallel support; checkpointing

Yes, OpenMx does have support for multithreading, with OpenMP. However, the package is only routinely tested with gcc and clang, not with the Mpi toolset. It might be worth trying to compile it without parallel, to see if that makes a difference.

Concerning checkpointing, was there a file written in R's working directory when the MxModel was run? That's where checkpointing output goes. It's possible there was no file written, since I don't know how well checkpointing works with the default mxOptions. You could try

factorModel <- mxOption(factorModel, "Always Checkpoint", "Yes")
factorModel <- mxOption(factorModel, "Checkpoint Units", "iterations")
factorModel <- mxOption(factorModel, "Checkpoint Count", 1)
factorModelFit <- mxRun(factorModel, checkpoint=TRUE)
Shesprich's picture
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Joined: 04/13/2017 - 11:44
checkpointing

Sorry about that I missed the extra file in the directory. I thought the checkpointing put additional output to the terminal. My bad.

Shane

p.s. I renamed the file to One Factor.txt since the site would not let me upload a file with extension omx

File attachments: 
jpritikin's picture
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Joined: 05/24/2012 - 00:35
trace

Ah, well, it looks like things are going wrong really early. Like Rob said, we don't do a lot of testing with MPI. If you need to make OpenMx work with MPI then you're going to need some software developers to figure out what is going wrong.

Shesprich's picture
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Joined: 04/13/2017 - 11:44
No OpenMpi

Sorry I haven't posted in a while, but I tried recompiling without using OpenMpi and that did fix the problems. So I'll just have to figure out what MPI is doing that is breaking things.

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