Similar compilation problems NWChem-6.6

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12:41:28 PM PST - Mon, Jan 18th 2016
Hello, I have been following posts and trying resolutions to my compilation problems but with still no joy. Specifically: Environment export NWCHEM_TARGET=x86_64 export NWCHEM_MODULES=all export USE_MPI=Y export USE_MPIF=Y export USE_MPIF4=Y export MPI_LOC="/opt/openmpi/1.8.4-intel15.0-noib" export MPI_INCLUDE="/opt/openmpi/1.8.4-intel15.0-noib/include" export MPI_LIB="/opt/openmpi/1.8.4-intel15.0-noib/lib" export LIBMPI="-lmpi_f90 -lmpi_f77 -lmpi -ldl -lm -Wl,--export-dynamic -lrt -lnsl -lutil -lm -ldl" export LARGE_FILES=TRUE export USE_NOFSCHECK=TRUE export HAS_BLAS=yes export USE_SCALAPACK=y export MKLLIB=/opt/intel/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64 export MKLINC=/opt/intel/compilers_and_libraries_2016.1.150/linux/mkl/include export BLASOPT="-L$MKLLIB -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm" export LAPACK_LIBS="-L$MKLLIB -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm" export SCALAPACK="-L$MKLLIB -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lmkl_blacs_intelmpi_ilp64 -lpthread -lm" export SCALAPACK_SIZE=8 export BLAS_SIZE=8 export FC=ifort export CC=icc With the following result: everything good until . . . configure: searching for MPI_TS... checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking for library containing MPI_Init... no configure: error: test for COMEX_NETWORK=MPI_TS failed configure: error: ../../ga-5-4/comex/configure failed for comex make: *** [build/config.status] Error 1 Thank you for any help.

Forum Vet

1:23:45 PM PST - Mon, Jan 18th 2016
Please try the following unset MPI_INCLUDE unset MPI_LIB unset LIBMPI export PATH=/opt/openmpi/1.8.4-intel15.0-noib/bin:$PATH unset FC unset CC cd $NWCHEM_TOP/src/tools rm -rf build install make FC=ifort If this still fails, please upload the following files to a website of your choice (e.g. dropbox, github, etc ...) $NWCHEM_TOP/src/tools/build/config.log $NWCHEM_TOP/src/tools/build/comex/config.log and send the output of the commands which mpif90 mpif90 -show

Clicked A Few Times

1:53:33 PM PST - Mon, Jan 18th 2016
NWChem
Thanks. config files are: https://github.com/proteindj/NWChem_compiling which mpif90 /opt/openmpi/1.8.4-intel15.0-noib/bin/mpif90 mpif90 -show ifort -I/opt/openmpi/1.8.4-intel15.0-noib/include -I/opt/openmpi/1.8.4-intel15.0-noib/lib -Wl,-rpath -Wl,/opt/openmpi/1.8.4-intel15.0-noib/lib -Wl,--enable-new-dtags -L/opt/openmpi/1.8.4-intel15.0-noib/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi

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2:07:18 PM PST - Mon, Jan 18th 2016
The config.log files are the result of the MPI_INCLUDE, MPI_LIB abd LIBMPI settings of your first post. Could you please follow my suggestions at post #2 http://nwchemgit.github.io/Special_AWCforum/sp/id6898 and send the config.log files after those changes?

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2:18:40 PM PST - Mon, Jan 18th 2016
Updated output of config files
Those files have now been updated via running with your suggestions. Thanks

Forum Vet

2:25:01 PM PST - Mon, Jan 18th 2016

C compiler not working correctly

After browsing your config.log files, you can seen from both logs that the C compiler you are using is not compatible with the MPI libraries you are using

configure:6807: cc -o conftest -g -O2    -I/opt/openmpi/1.8.4-intel15.0-noib/include -I/opt/openmpi/1.8.4-intel15.0-noib/lib -I/opt/openmpi/1.8.4-intel15.0-noib/include    -L/opt/openmpi/1.8.4-intel15.0-noib/lib -L/opt/openmpi/1.8.4-intel15.0-noib/lib conftest.c    -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi >&5
/opt/openmpi/1.8.4-intel15.0-noib/lib/libmpi_usempif08.so: undefined reference to `_intel_fast_memmove'
/opt/openmpi/1.8.4-intel15.0-noib/lib/libmpi_usempif08.so: undefined reference to `tbk_string_stack_signal_impl'

A possible solution would be to use icc to compile the tools. Please try the following

cd $NWCHEM_TOP/src/tools
rm -rf build install
make FC=ifort CC=icc

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7:06:34 AM PST - Tue, Jan 19th 2016
cc and icc the same result
Thanks but I get a similar result with FC and CC redefined for intel versions, i.e. configure:6807: icc -o conftest -g -O2 -I/opt/openmpi/1.8.4-intel15.0-noib/include -I/opt/openmpi/1.8.4-intel15.0-noib/include -L/opt/openmpi/1.8.4-intel15.0-noib/lib -Wl,--export-dynamic -L/opt/openmpi/1.8.4-intel15.0-noib/lib conftest.c -lmpi_mpifh -lmpi_usempif08 -lmpi -ldl -lm -lrt -lnsl -lutil -lm -ldl >&5 /opt/openmpi/1.8.4-intel15.0-noib/lib/libmpi_usempif08.so: undefined reference to `_intel_fast_memmove' /opt/openmpi/1.8.4-intel15.0-noib/lib/libmpi_usempif08.so: undefined reference to `tbk_string_stack_signal_impl'

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12:53:42 PM PST - Tue, Jan 19th 2016
A little bit further along, now catastrophic error: MIC
Now from the make log file: (thanks for your support) ifort -c -g -I. -I/opt/openmpi/1.8.4-intel15.0-noib//include -I/ihome/djewell/nwchem/nwchem-6.6/src/include -I/ihome/djewell/nwchem/nwchem-6.6/src/tools/install/include -DSCALAPACK -DPARALLEL_DIAG -DNOFSCHECK -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/ihome/djewell/nwchem/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -DJOBTIMEPATH=\"/ihome/djewell/nwchem/nwchem-6.6/bin/x86_64\" -DNWCHEM_SRCDIR="\"/ihome/djewell/nwchem/nwchem-6.6/src\"" util_units.F ifort -c -g -I. -I/opt/openmpi/1.8.4-intel15.0-noib//include -I/ihome/djewell/nwchem/nwchem-6.6/src/include -I/ihome/djewell/nwchem/nwchem-6.6/src/tools/install/include -DSCALAPACK -DPARALLEL_DIAG -DNOFSCHECK -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/ihome/djewell/nwchem/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -DJOBTIMEPATH=\"/ihome/djewell/nwchem/nwchem-6.6/bin/x86_64\" -DNWCHEM_SRCDIR="\"/ihome/djewell/nwchem/nwchem-6.6/src\"" util_intrsc2008.F icc -c -I. -I/opt/openmpi/1.8.4-intel15.0-noib//include -I/ihome/djewell/nwchem/nwchem-6.6/src/include -I/ihome/djewell/nwchem/nwchem-6.6/src/tools/install/include -DSCALAPACK -DPARALLEL_DIAG -DNOFSCHECK -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/ihome/djewell/nwchem/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -DJOBTIMEPATH=\"/ihome/djewell/nwchem/nwchem-6.6/bin/x86_64\" -DNWCHEM_SRCDIR="\"/ihome/djewell/nwchem/nwchem-6.6/src\"" -g -o util_fadvise.o util_fadvise.c icc -c -I. -I/opt/openmpi/1.8.4-intel15.0-noib//include -I/ihome/djewell/nwchem/nwchem-6.6/src/include -I/ihome/djewell/nwchem/nwchem-6.6/src/tools/install/include -DSCALAPACK -DPARALLEL_DIAG -DNOFSCHECK -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/ihome/djewell/nwchem/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -DJOBTIMEPATH=\"/ihome/djewell/nwchem/nwchem-6.6/bin/x86_64\" -DNWCHEM_SRCDIR="\"/ihome/djewell/nwchem/nwchem-6.6/src\"" -g -o util_mic_support.o util_mic_support.c icc: warning #10362: Environment configuration problem encountered. Please check for proper MPSS installation and environment setup. util_mic_support.c(4): catastrophic error: MIC cannot open source file "stdio.h" #include <stdio.h> ^ compilation aborted for util_mic_support.c (code 4) make[1]: * [/ihome/djewell/nwchem/nwchem-6.6/lib/x86_64/libnwcutil.a(util_mic_support.o)] Error 4 make[1]: Leaving directory `/ihome/djewell/nwchem/nwchem-6.6/src/util' make: * [libraries] Error 1

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2:36:09 PM PST - Tue, Jan 19th 2016
MIC
Do you have Intel Xeon Phi (aka MIC) hardware on your system?

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1:51:26 PM PST - Wed, Jan 20th 2016
Thought I did but - No Xeon Phi
The admin tells me we don't have Xeon Phi. I will try without specifying Xeon Phi

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8:27:46 AM PST - Thu, Jan 21st 2016
Compile completed but - error while loading shared libraries:
./nwchem: error while loading shared libraries: libmkl_scalapack_ilp64.so: cannot open shared object file: No such file or directory Thank you for your help

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8:50:21 AM PST - Thu, Jan 21st 2016
OK- module loading was the problem
mkl/11.3

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8:36:31 AM PST - Fri, Jan 22nd 2016

SEQ Fault running newly compiled NWChem 6.6

Hi, thanks for any help

test run of installed nwchem:

nwchem my_h2o_scf.nw

argument  1 = my_h2o_scf.nw

.
.
.

     Superposition of Atomic Density Guess

     -------------------------------------



Sum of atomic energies:         -75.76222910

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
nwchem 0000000003313D11 Unknown Unknown Unknown
nwchem 0000000003312467 Unknown Unknown Unknown
libmpi_usempif08. 00002AD8E14E07B2 Unknown Unknown Unknown
libmpi_usempif08. 00002AD8E14E0606 Unknown Unknown Unknown
libmpi_usempif08. 00002AD8E14CEE5C Unknown Unknown Unknown
libmpi_usempif08. 00002AD8E14AFFA8 Unknown Unknown Unknown
libpthread.so.0 00000036F260F790 Unknown Unknown Unknown
libmpi.so.1 00002AD8E1C7D0B9 Unknown Unknown Unknown
libmkl_blacs_inte 00002AD8E121BA39 Unknown Unknown Unknown
libmkl_blacs_inte 00002AD8E121A1CD Unknown Unknown Unknown
libmkl_blacs_inte 00002AD8E120B522 Unknown Unknown Unknown
libmkl_blacs_inte 00002AD8E120AEF1 Unknown Unknown Unknown
libmkl_blacs_inte 00002AD8E12395FB Unknown Unknown Unknown
nwchem 00000000031E8C05 Unknown Unknown Unknown
nwchem 0000000000A024C3 Unknown Unknown Unknown
nwchem 0000000000A1B42C Unknown Unknown Unknown
nwchem 0000000000A0379E Unknown Unknown Unknown
nwchem 0000000000424009 Unknown Unknown Unknown
nwchem 0000000001AEB592 Unknown Unknown Unknown
nwchem 000000000118B97E Unknown Unknown Unknown
nwchem 000000000118865D Unknown Unknown Unknown
nwchem 000000000042B4F8 Unknown Unknown Unknown
nwchem 00000000004167BF Unknown Unknown Unknown
nwchem 000000000040B087 Unknown Unknown Unknown
nwchem 000000000040AB9E Unknown Unknown Unknown
libc.so.6 00000036F1E1ED5D Unknown Unknown Unknown
nwchem 000000000040AAA9 Unknown Unknown Unknown

Clicked A Few Times

8:36:47 AM PST - Fri, Jan 22nd 2016

SEQ Fault running newly compiled NWChem 6.6

Hi, thanks for any help

test run of installed nwchem:

nwchem my_h2o_scf.nw

argument  1 = my_h2o_scf.nw

.
.
.

     Superposition of Atomic Density Guess

     -------------------------------------



Sum of atomic energies:         -75.76222910

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