Install fails on MacOS X, linker error: Symbol not found: __gfortran_pow_r8_i4
roffe
Joined: 03/10/2013
These are the last relevant error message lines:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/opt/local/Library/Frameworks/R.framework/Versions/2.15/Resources/library/OpenMx/libs/x86_64/OpenMx.so':
dlopen(/opt/local/Library/Frameworks/R.framework/Versions/2.15/Resources/library/OpenMx/libs/x86_64/OpenMx.so, 6): Symbol not found: __gfortran_pow_r8_i4
Referenced from: /opt/local/Library/Frameworks/R.framework/Versions/2.15/Resources/library/OpenMx/libs/x86_64/OpenMx.so
Expected in: dynamic lookup
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/opt/local/Library/Frameworks/R.framework/Versions/2.15/Resources/library/OpenMx’
According to a Google search, this error message is a) rare and b) is caused by __gfortran_pow_r8_i4 having been removed from recent versions of gfortran.
Any and all pointers to solutions appreciated. Thank you.
__gfortran_pow_r8_i4
http://people.virginia.edu/~jnp3bc/libnpsol-svn177.a
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In reply to __gfortran_pow_r8_i4 by jpritikin
Seems we're not on quite the same architecture:
cp ~/Downloads/libnpsol-svn177.a ~/OpenMx/inst/npsol/osx/libnpsol.a
sudo R CMD INSTALL -i ~/OpenMx
...
ld: warning: ignoring file ../inst/npsol/osx/libnpsol.a, file was built for archive which is not the architecture being linked (x86_64): ../inst/npsol/osx/libnpsol.a
I'm on a 64-bit Mac, don't know if that is significant. I'm also not overly confident that I'm doing this right.
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In reply to Seems we're not on quite the same architecture: by roffe
npsol
If you are willing to recompile npsol for your architecture, please join https://lists.virginia.edu/sympa/info/openmx-developers
Sorry I don't have better news.
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In reply to npsol by jpritikin
I just replied above in this
- roll back npsol and F77 to a version that will compile OpenMX on a 64-bit mac
- tweak the makefile to build a statically linked binary
- package that up for redistribution on the website
- or, even better, adapt the installation process to pull the static binary if it is installing on OS X
I cannot do this right now. However, whoever is refactoring npsol probably has the knowledge to perform this task.
Thanks,
Ian
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In reply to I just replied above in this by iandennismiller
No problems with 64bit mac
I resolved the earlier compilation problems with R2.15. Essentially I was having trouble with too many gcc's installed. Cleaning them all out and using fresh xcode install solved the issue. Gfortran works fine. One trick I found was that R on the command line should point to R64, per the end bit of the wiki for developer.
If you are not a developer, the binary install should work fine for a 64 bit install (parallel or not)
source("http://openmx.psyc.virginia.edu/getOpenMx.R")
And... replacement for npsol is on its way!
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In reply to No problems with 64bit mac by neale
no dice with gcc 4.7
Thanks for checking into this. I've tried the developer instructions, including the patched npsol from subversion. The core issue is with gfortran; my version is too new:
gfortran --version
GNU Fortran (GCC) 4.7.2
Copyright (C) 2012 Free Software Foundation, Inc.
Please see the following; npsol has probably been broken in some way since gcc 4.3 (i.e. gfortran 4.2 may be the last version that worked):
http://gcc.gnu.org/ml/fortran/2009-05/msg00404.html
I was at the APS conference over the weekend and I spoke with several members of the OpenMX team. I am trying to build OpenMx using an older version of fortran. So far, so good, but I do not have a full version building yet. You can track my progress here:
https://github.com/iandennismiller/openmx-osx
Also, I am a little confused here... It really looks like there is a pre-compiled binary distro already available:
http://openmx.psyc.virginia.edu/packages/bin/macosx/universal/contrib/2.15/
However, that appears to be broken too. First off, it does not install using the following process because the suffix is .tgz instead of .tar.gz:
install.packages(pkgs=c('OpenMx'), contriburl='http://openmx.psyc.virginia.edu/packages/bin/macosx/universal/contrib/2.15')
Then, using my own mirror (with a correctly named tarball) to install it like so:
install.packages(pkgs=c('OpenMx'), contriburl='http://imiller.utsc.utoronto.ca/p/OpenMx')
I receive the following error:
Error: package ‘OpenMx’ was built for universal-apple-darwin9.8.0
...so I still believe that if somebody (maybe you) can just build and statically link the thing on a modern OS X system, then make the correctly named tarball (.tar.gz, apparently) available via http://openmx.psyc.virginia.edu/packages/bin/macosx/universal/contrib/2.15, I could possibly install OpenMx without having to build an old version of gcc in order to compile it.
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In reply to no dice with gcc 4.7 by iandennismiller
Works for me on 4.8.1
new-host% gfortran --version
GNU Fortran (GCC) 4.8.1 20130404 (prerelease)
Copyright (C) 2013 Free Software Foundation, Inc.
Which version of R are you using? What does
which R return, and what does that point to? I had to go through a few steps to see where it was eventually headed, for which purpose I used a few doses of awk (seems clumsy but piping things into ls doesn't work)
which R | awk '{print "ls -lF",$0}' | csh | awk '{print "ls -lF",$NF}' | csh
on my system I got
new-host% which R | awk '{print "ls -lF",$0}' | csh | awk '{print "ls -lF",$NF}' | csh
lrwxr-xr-x 1 root admin 3 May 27 08:22 /Library/Frameworks/R.framework/Resources/bin/R@ -> R64
and it works fine.
I don't think that static linking is an option - and I don't think it's needed.
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In reply to Works for me on 4.8.1 by neale
Symbol not found: __gfortran_pow_r8_i4
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/OpenMx/libs/OpenMx.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/OpenMx/libs/OpenMx.so, 6): Symbol not found: __gfortran_pow_r8_i4
Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/OpenMx/libs/OpenMx.so
Expected in: dynamic lookup
Error: loading failed
Qeb search suggests that the culprit symbol embedded in NPSOL may reflect compilation using Fortran 4.4 or older and no longer supported? e.g.
http://marc.info/?l=gcc-fortran&m=136205999713783
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In reply to __gfortran_pow_r8_i4 by jpritikin
results of compilation
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Users/idm/Library/R/Versions/2.15/OpenMx/libs/OpenMx.so':
dlopen(/Users/idm/Library/R/Versions/2.15/OpenMx/libs/OpenMx.so, 6): Symbol not found: _npoptn_
Referenced from: /Users/idm/Library/R/Versions/2.15/OpenMx/libs/OpenMx.so
Expected in: dynamic lookup
It appears npoptn might be something else related to F77 and npsol?
At any rate, it sounds like OpenMX is broken on OS X. Is there any possible workaround, like a statically linked version or an older version, or maybe instructions for using a suitable fortran compiler? Any help would be appreciated.
In the meanwhile, Linux is still working, so I'm still going to get all my work done on time. However, I'm eager to know if I can do this on OS X.
Thanks!
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In reply to results of compilation by iandennismiller
Is this R 2.15 problem
2. It is the case that npoptn is part of npsol.
3. You can of course run OpenMx on OSX simply by downloading and installing the binary. It seems that it is only compiling that seems to be broken, and perhaps only on R 2.15, and even then maybe it is something to do with the compiler version.
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In reply to Is this R 2.15 problem by neale
R 2.15 problem with make install
new-host-4% sudo make install
rm -rf build/*
mkdir -p build
cp DESCRIPTION DESCRIPTION.bak
sed '/Version:/d' DESCRIPTION.bak > DESCRIPTION
echo "Version: "999.0.0"-"2465 >> DESCRIPTION
cd build; R CMD build ..
Welcome to R on Mike Neale's Macbook!
* checking for file ‘../DESCRIPTION’ ... OK
* preparing ‘OpenMx’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
Removed empty directory ‘OpenMx/docs/source/static/Rdoc’
Removed empty directory ‘OpenMx/docs/source/static/demo’
Removed empty directory ‘OpenMx/docs/source/static’
Removed empty directory ‘OpenMx/docs/source/templates’
Removed empty directory ‘OpenMx/inst/unit-tests’
Removed empty directory ‘OpenMx/models/failing/temp-files’
Removed empty directory ‘OpenMx/testsuite’
* looking to see if a ‘data/datalist’ file should be added
* re-saving tabular files
* building ‘OpenMx_999.0.0-2465.tar.gz’
mv DESCRIPTION.bak DESCRIPTION
rm -f man/genericFitDependencies.Rd man/imxAddDependency.Rd man/MxAlgebraFunction.Rd \
man/omxCheckCloseEnough.Rd
cd build; R CMD INSTALL "--configure-args=--enable-openmp" OpenMx_999.0.0-2465.tar.gz
Welcome to R on Mike Neale's Macbook!
* installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
* installing *source* package ‘OpenMx’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gcc option to support OpenMP... -fopenmp
checking whether gcc is installed... yes
checking build system type... i386-apple-darwin12.3.0
checking host system type... i386-apple-darwin12.3.0
checking for inst/npsol/osx/libnpsol.a... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: executing src/omxSymbolTable.h commands
config.status: executing src/omxSymbolTable.c commands
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Wall -fopenmp -mmacosx-version-min=10.4 -fPIC -g -O2 -c merge.c -o merge.o
gcc: error: x86_64: No such file or directory
gcc: error: unrecognized option '-arch'
make[1]: *** [merge.o] Error 1
ERROR: compilation failed for package ‘OpenMx’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/OpenMx’
make: *** [install] Error 1
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In reply to R 2.15 problem with make install by neale
Well, one suggestion is to
I've concluded (perhaps incorrectly) that there is no way to compile this with a contemporary distribution of F77, so unless npsol is majorly refactored out, this isn't going to lead anywhere. I think the best bet is to try to compile against an older version, then statically link against the older F77 and npsol so as to distribute a fully working, fully self-contained package.
For the sake of novice users, it would be great to adapt this to the current install process. However, I'd be personally happy to install it manually.
Ian
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