From NWChem
Viewed 1818 times, With a total of 3 Posts
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Just Got Here
Threads 1
Posts 2
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| 7:33:39 AM PST - Thu, Dec 12th 2013 |
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Dear all,
I am new in NWChem and I am trying to compile it on my local machine (x86_64) using MKL intel library, openmpi-intel and as compiler gfortran.
After the installation I got the executable but when I try to make a test I got a segmentation fault error like:
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Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
- 0 0x2B33F98126C7
- 1 0x2B33F9812C94
- 2 0x2B33FAF91D9F
- 3 0x2B33FAFA4EAC
- 4 0x2B33FAFABF58
- 5 0x2B6FE0C in dassertp_fail.part.0 at armci.c:0
- 6 0x2B70E19 in PARMCI_Init
- 7 0x2B0AA7D in pnga_initialize
- 8 0x51076E in nwchem at nwchem.F:124
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Apparently the library are linked correctly but probably I am missing something for a correct compiling.
I would appreciate some help and I can give both make.log file and config.log as well
Thank you so much
Daniele
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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Forum Vet
Threads 7
Posts 1152
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| 11:00:26 AM PST - Thu, Dec 12th 2013 |
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Daniele
It's hard to tell what went wrong in your installation, more details would help in diagnosing the problem.
Could you please send us (or upload to a website) the following files (2 or 3 might be missing):
1) $NWCHEM_TOP/src/tools/build/config.log
2) $NWCHEM_TOP/src/tools/build/armci/config.log
3) $NWCHEM_TOP/src/tools/build/comex/config.log
Could you also send us:
a) list of env. variables used
b) compilation command used (e.g. make FC=ifort)
Thanks, Edo
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Just Got Here
Threads 1
Posts 2
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| 6:32:50 AM PST - Tue, Dec 17th 2013 |
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Dear Edo, thank you so much for your help.
Regarding points a) and b):
a) environment variable, here below what I am using:
setenv LARGE_FILES TRUE
setenv USE_NOFSCHECK TRUE
setenv LIB_DEFINES -DDFLT_TOT_MEM=16777216
setenv NWCHEM_TARGET LINUX64
setenv ARMCI_NETWORK MPI-MT
setenv NWCHEM_MODULES all
setenv MRCC_THEORY TRUE
setenv USE_SCALAPACK y
- link to the libraries
setenv MKL "/usr/users/bin/intel/mkl/10.2.7.041/lib/em64t"
setenv BLASOPT "-L${MKL} -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread -lm"
setenv LAPACK_LIB "-L${MKL} -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread -lm"
setenv SCALAPACK "-L${MKL} -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm"
b) as a compiler I am using gfortran (make FC=gfortran >& make.log)
I checked and I have all the three config.lof files.
How can I upload or send you these files, I wouldn't copy and paste here because are quite large.
Usually the warnings that I have in the three config.log are:
- conftest.c:117:53: warning: integer overflow in expression [-Woverflow]
- conftest.c:118:6: warning: conflicting types for built-in function 'fork' [enabled by default]
- conftest.c:116:6: warning: conflicting types for built-in function 'floor' [enabled by default]
- the same as above for 'modf', 'pow', 'sqrt', 'hypot', 'bcopy', 'bzero', 'memcpy', 'memset' and others
- cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C [enabled by default]
Thank you so much for your help and patient!
Daniele
%%
Daniele
It's hard to tell what went wrong in your installation, more details would help in diagnosing the problem.
Could you please send us (or upload to a website) the following files (2 or 3 might be missing):
1) $NWCHEM_TOP/src/tools/build/config.log
2) $NWCHEM_TOP/src/tools/build/armci/config.log
3) $NWCHEM_TOP/src/tools/build/comex/config.log
Could you also send us:
a) list of env. variables used
b) compilation command used (e.g. make FC=ifort)
Thanks, Edo
%%
Quote:Edoapra Dec 12th 6:00 pmDaniele
It's hard to tell what went wrong in your installation, more details would help in diagnosing the problem.
Could you please send us (or upload to a website) the following files (2 or 3 might be missing):
1) $NWCHEM_TOP/src/tools/build/config.log
2) $NWCHEM_TOP/src/tools/build/armci/config.log
3) $NWCHEM_TOP/src/tools/build/comex/config.log
Could you also send us:
a) list of env. variables used
b) compilation command used (e.g. make FC=ifort)
Thanks, Edo |
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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Forum Vet
Threads 7
Posts 1152
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| 10:22:16 AM PST - Tue, Dec 17th 2013 |
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Sorry, If I cannot be of much help since I didn't get all the information I was looking for.
The only suggestion I can give is to replace ARMCI_NETWORK=MPI-MT with MPI-TS.
We rarely use MPI-MT, while MPI-TS has been thoroughly validated and it relies on much more readily available MPI functionality
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