From NWChem
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2:39:34 AM PDT - Wed, Apr 25th 2018 |
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Hi There,
I'm trying to use NWChem with ChemShell to perform QM/MM simulations. To link these two programs, NWChem has to be compiled with MPI, Intel compilers & using the 64_to_32 flag.
I'm using the latest version on the GitHub branch since Edo had to make a quick fix for me to use the dispersion XDM correctly.
The make log attached 'my_make_ifort.log' shows and error at the bottom, line 765:
'checking for library containing MPI_Init... no
configure: error: test for COMEX_NETWORK=MPI_TS failed
configure: error: ../../ga-5.6.5/comex/configure failed for comex'
I've tried using different flags such as MPI-PR and they still fail. In addition, a developer from ChemShell (Tom) said that using a ARMCI NETWORK other than TS causes errors 'tom_email.txt'.
The following link contains a tarball
My compile script: my-nwchem.sh
My make log: my_make_ifort.log
The auto generated configure log: config.log
Some guidelines written by chemshell developer (These were for NWChem6.6): tom_email.txt
https://drive.google.com/open?id=18Xzkez3_tZs5LdBg9_dp0JydBd_aIePq
Any idea how can avoid this error and compile NWChem correctly would be greatly appreciated.
Best,
Alex
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Edited On 9:44:27 AM PDT - Wed, Apr 25th 2018 by Gh3orghiu
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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9:44:59 AM PDT - Wed, Apr 25th 2018 |
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Alex
I see plenty of issues with your settings
I would start from scratch (that is by unsetting all the env. variables you are using) and use the simpler instructions described at
https://github.com/nwchemgit/nwchem/wiki/Compiling-NWChem#example-nersc-cori
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9:46:31 AM PDT - Wed, Apr 25th 2018 |
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ARCHER Compile Success
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With the help of ARCHER support team, I believe I've managed to get this to work now.
Here is the following script:
#!/bin/bash
set -e
export NWCHEM_TOP=...
# TomK's email
export LD=/usr/bin/ld
module swap PrgEnv-cray PrgEnv-intel/5.1.29
module swap intel intel/15.0.2.164
module swap cray-mpich/7.5.5 cray-mpich/7.2.6
module unload cray-libsci
# Fix SSL errors
module load openssl
module load git
module load wget
# Fix ga-5.6.5 failing to create configure script
# May be unneeded - original failure possibly due to "make -j12" instead
module load autotools
# MPI Setup
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export LIBMPI=" "
export MPI_LIB=$MPICH_DIR/lib
export MPI_INCLUDE=$MPICH_DIR/inc
# NWChem stuff
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all
export LARGE_FILES=TRUE
export USE_64TO32=y
export ARMCI_NETWORK=MPI-TS
# BLAS and ScaLAPACK
export HAS_BLAS=y
export USE_SCALAPACK=y
export BLAS_SIZE=4
export LAPACK_SIZE=4
export SCALAPACK_SIZE=4
# lp for 32-bit libraries
export SCALAPACK="-L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lmkl_blacs_intelmpi_lp64 -lpthread -lm"
export BLASOPT="-L$MKLROOT/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lmkl_core -lmkl_intel_thread -lpthread -lm"
# required to prevent compiler error
export USE_OPENMP=y
# Compilers
export FC=ftn
export _FC=ifort
export CC=cc
export _CC=icc
export CRAYPE_LINK_TYPE=dynamic
cd $NWCHEM_TOP/src
make clean
make nwchem_config 2>&1 | tee nwchem_config.log
make -j12 64_to_32
#make -j12 2>&1 | tee nwchem_build.log
# Parallel make causes errors here
make 2>&1 | tee nwchem_build.log
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Edited On 9:47:15 AM PDT - Wed, Apr 25th 2018 by Gh3orghiu
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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10:39:19 AM PDT - Wed, Apr 25th 2018 |
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ARMCI_NETWORK=MPI-TS will result in extremely poor performance on Archer. I would encourage you to follow the instructions in the nwchem github wiki to get ARMCI_NETWORK=MPI-PR to work
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10:54:55 AM PDT - Wed, Apr 25th 2018 |
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Incorrectly linked libraries with LD
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Just worth mentioning that to get this to work, requires the following environments to be set in submission script.
export LD=/usr/bin/ld
export LD_LIBRARY_PATH="/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64/:/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64"
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10:58:15 AM PDT - Wed, Apr 25th 2018 |
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Quote:Edoapra Apr 25th 10:39 amARMCI_NETWORK=MPI-TS will result in extremely poor performance on Archer. I would encourage you to follow the instructions in the nwchem github wiki to get ARMCI_NETWORK=MPI-PR to work
Thank you for letting me know this is the case. However, I am trying to link NWChem with ChemShell and that supposedly has a problem with MPI-PR.
I'll talk to the ChemShell developers and let them know.
Alex
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