libmpc.so.3 and conda package

[apastore]

Hi I am trying to install misopy on hal and I am getting this error. any suggestion?

conda skeleton pipit misopy go well but when I build the package i get this error even if /opt/gnu/mpc/lib/ is in LD_LIBRARY_PATH

conda build misopy

gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DHAVE_RINTF=1 -DHAVE_FINITE=1 -DHAVE_EXPM1=1 -DHAVE_RINT=1 -DHAVE_LOG2=1 -DHAVE_LOGBL=1 -DHAVE_SNPRINTF=1 -DHAVE_LOG1P=1 -DHAVE_ROUND=1 -DHAVE_FMIN=1 -Ipysplicing/include -Ipysplicing/src/lapack -Ipysplicing/src/f2c -I/cbio/cslab/home/pastore/nobackup/bcbio/anaconda/envs/_build/include/python2.7 -c pysplicing/src/assignment.c -o build/temp.linux-x86_64-2.7/pysplicing/src/assignment.o /opt/gnu/gcc/4.8.1/libexec/gcc/x86_64-unknown-linux-gnu/4.8.1/cc1: error while loading shared libraries: libmpc.so.3: cannot open shared object file: No such file or directory error: command 'gcc' failed with exit status 1 Command failed: /bin/bash -x -e /cbio/cslab/home/pastore/misopy/build.sh

Thanks!

[tatarsky]

LD_LIBRARY_PATH is a runtime directive. Not a compiler link time directive.

What happens if you add -L/opt/gnu/mpc/lib to you line above.

(Will be a delay in answer by me this evening so give it a try and report back)

[tatarsky]

Also provide please the output of module list

[apastore]

module list Currently Loaded Modulefiles: 1) gcc/4.8.1 2) mpich2_eth/1.5

On Mar 4, 2016, at 5:28 PM, tatarsky notifications@github.com wrote:

module list

[tatarsky]

ALso I believe if you don't have direct control of the compiler generation of the options the environment var LIBRARY_PATH can provide a search path. You could try that as well.

https://gcc.gnu.org/onlinedocs/gcc/Environment-Variables.html

[jchodera]

conda build ignores local environment. We haven't found a way to get it to work with the gcc compilers on hal because of their shared library dependence on libmpc.

You can add gcc as a build: dependency in your meta.yaml for the conda recipe to work around this.

[tatarsky]

Hmm. When the dust clears on this cluster upgrade I'll take a look at the current gcc module. I noted I similar matter when doing the caffe work and while I dealt with it the module dependencies seemed overly complicated.

[apastore]

Thanks!

Sent from my iPhone

On Mar 5, 2016, at 6:20 PM, John Chodera notifications@github.com wrote:

conda build ignores local environment. We haven't found a way to get it to work with the gcc compilers on hal because of their shared library dependence on libmpc.

You can add gcc as a build: dependency in your meta.yaml for the conda recipe to work around this.

— Reply to this email directly or view it on GitHub.

[tatarsky]

I hope to have the gcc 4.8.5 module shortly. Just cleaning some items from upgrade still

[apastore]

thanks! At the and I just manage to install after a clean miniconda install ( I had some python path defined prior to miniconda install)

On Mar 15, 2016, at 3:20 PM, tatarsky notifications@github.com wrote:

I hope to have the gcc 4.8.5 module shortly. Just cleaning some items from upgrade still

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/cBio/cbio-cluster/issues/383#issuecomment-196982578

[tatarsky]

Ok. I can skip for now and announce a gcc 4.8.5 for testing separately if good with you....

[apastore]

Thanks! I just fix it before the restart and than it get out of my mind!

On Mar 15, 2016, at 3:25 PM, tatarsky notifications@github.com wrote:

Ok. I can skip for now and announce a gcc 4.8.5 for testing separately if good with you....

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/cBio/cbio-cluster/issues/383#issuecomment-196984651

[tatarsky]

Noted!