OpenMx Installation on Redhat Cluster
Shesprich
Joined: 04/13/2017
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
CXX1X CXX11
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In reply to CXX1X CXX11 by AdminJosh
CXX1X
> 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 ‘str’ with 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
Compute.cpp:899:13: error: request for member ‘size’ in ‘str’, which is of non-class type ‘int’
Compute.cpp:900:55: error: request for member ‘c_str’ in ‘str’, 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
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In reply to CXX1X by Shesprich
mpic++
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mpic++
Shane
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In reply to mpic++ by Shesprich
gcc version
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OpenMx Compiled but won't run properly
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++11’ is 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++11’ is 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++11’ is 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++11’ is 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++11’ is 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
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In reply to OpenMx Compiled but won't run properly by Shesprich
warning, not error; compilation probably OK
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 (usesummary(factorModelFit))?Log in or register to post comments
In reply to warning, not error; compilation probably OK by AdminRobK
Outputs
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
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In reply to Outputs by Shesprich
maybe there IS a compilation problem
Hmm, OK, there definitely seems to be something wrong here.
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Parallel?
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.
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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
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still broken?
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Mx in Parallel/still broken?
mpic++ -showme, mpicc -showme:compile and mpicc -showme:linkwere acceptable or if there was something wrong with them. Finally here is an output from the sample simulation using checkpoint=TRUEcat 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
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In reply to Mx in Parallel/still broken? by Shesprich
checkpoint
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In reply to Mx in Parallel/still broken? by Shesprich
parallel support; checkpointing
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)
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checkpointing
Shane
p.s. I renamed the file to One Factor.txt since the site would not let me upload a file with extension omx
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In reply to checkpointing by Shesprich
trace
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No OpenMpi
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