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