Neuron 7.4 installation on cluster - missing "inithoc.o"

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catubc
Posts: 21
Joined: Mon Apr 07, 2014 6:46 pm

Neuron 7.4 installation on cluster - missing "inithoc.o"

Post by catubc » Fri Jun 12, 2015 5:58 pm

Dear All

I'm working on installing 7.4-release on a cluster. Currently I'm having an issue that's probably very close to the end of the job. The error I get is:

icpc: error #10236: File not found: 'build/temp.linux-x86_64-2.7/inithoc.o'

Any suggestions? I thought maybe I'm not loading all the correct modules for compilation time. But I don't see what is missing.

Here's the last 100 lines or so of output:

***********************************************
copying /home/s/swindale/catalin/nrn/share/nrn/lib/python/neuron/rxd/initializer.py -> build/lib.linux-x86_64-2.7/neuron/rxd
running build_ext
building 'neuron.hoc' extension
creating build/temp.linux-x86_64-2.7
mpicc -fno-strict-aliasing -fp-model precise -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -I../.././src/oc -I../oc -I../.././src/nrnmpi -I/scinet/gpc/tools/Python/Python278-shared-intel/include/python2.7 -c inithoc.cpp -o build/temp.linux-x86_64-2.7/inithoc.o
In file included from /scinet/gpc/tools/Python/Python278-shared-intel/include/python2.7/Python.h(8),
from inithoc.cpp(6):
/scinet/gpc/tools/Python/Python278-shared-intel/include/python2.7/pyconfig.h(1182): warning #47: incompatible redefinition of macro "_POSIX_C_SOURCE" (declared at line 162 of "/usr/include/features.h")
#define _POSIX_C_SOURCE 200112L
^

In file included from /scinet/gpc/tools/Python/Python278-shared-intel/include/python2.7/Python.h(8),
from inithoc.cpp(6):
/scinet/gpc/tools/Python/Python278-shared-intel/include/python2.7/pyconfig.h(1204): warning #47: incompatible redefinition of macro "_XOPEN_SOURCE" (declared at line 164 of "/usr/include/features.h")
#define _XOPEN_SOURCE 600
^

mpic++ -pthread -shared build/temp.linux-x86_64-2.7/inithoc.o -L/home/s/swindale/catalin/nrn/x86_64/lib -L. -L/scinet/gpc/tools/Python/Python278-shared-intel/lib -lnrnpython -lnrnoc -loc -lnrniv -livoc -lmemacs -lmeschach -lneuron_gnu -lnrnmpi -lscopmath -lsparse13 -lsundials -lreadline -livos -lpython2.7 -o build/lib.linux-x86_64-2.7/neuron/hoc.so -Wl,-R/home/s/swindale/catalin/nrn/x86_64/lib -Wl,-R.
icpc: error #10236: File not found: 'build/temp.linux-x86_64-2.7/inithoc.o'
error: command 'mpic++' failed with exit status 1
make[3]: *** [install-exec-hook] Error 1
make[3]: Leaving directory `/home/s/swindale/catalin/nrn'
make[2]: *** [install-exec-am] Error 2
make[2]: Leaving directory `/home/s/swindale/catalin/nrn'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/home/s/swindale/catalin/nrn'
make: *** [install-recursive] Error 1
gpc-f103n084-ib0-$

hines
Site Admin
Posts: 1577
Joined: Wed May 18, 2005 3:32 pm

Re: Neuron 7.4 installation on cluster - missing "inithoc.o"

Post by hines » Sun Jun 14, 2015 12:46 pm

It looks to me that what is failing is a piece that is only needed if you launch python instead of nrniv to run NEURON.
Try again with the configure you used but with the additional argument:
--disable-pysetup

If this does not work or something else is unsuccessful, let's take this to email. Send to michael dot hines at yale dot edu

hines
Site Admin
Posts: 1577
Joined: Wed May 18, 2005 3:32 pm

Re: Neuron 7.4 installation on cluster - missing "inithoc.o"

Post by hines » Sun Jun 14, 2015 1:02 pm

Of course, if you do have a strong preference for launching python instead of nrniv ...
it is a bit surprising that the warnings about incompatible redefinition of macro were called warnings instead of errors since they seemed to prevent success in building inithoc.o
Unfortunately, it is even more puzzling that pyconfig.h and features.h can be incompatible in this way and I don't see offhand why inithoc.cpp could cause that.
However, if you are willing to experiment a bit, I'd try moving line #include <Python.h>
to the top of the file

catubc
Posts: 21
Joined: Mon Apr 07, 2014 6:46 pm

Re: Neuron 7.4 installation on cluster - missing "inithoc.o"

Post by catubc » Tue Jun 16, 2015 1:15 am

Michael

So NEURON 7.4 seems to compile and run on my own workstation.

I think there's something odd about the multiple versions of python used on the clusters. I assume that's what the "-2.7" in the error line stands for, i.e. some version of python.

Give me a couple of days to work with tech people, they seem to think they can install it.

Thanks,
catubc

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