From NWChem
Viewed 2044 times, With a total of 1 Posts
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Just Got Here
Threads 1
Posts 2
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| 10:22:02 AM PST - Fri, Feb 5th 2016 |
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Hello,
I am trying to compile nwchem-6.6 with mkl libraries (blas, lapack, scalapack) and openmpi_1.10ifort.
The main problem is that openmpi is not found.
"checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from icc object... forrtl: severe (24): end-of-file during read, unit 5, file stdin .. " and
"checking for mpirun... /software/mpi/openmpi_1.10ifort/bin/mpirun
forrtl: severe (24): end-of-file during read, unit 5, file stdin, line 240"
and at end: many "undefined reference" and "function not been used"
Anyone knows what i can do, that the code compiles properly?
Installation and log file are in following folder:
https://www.dropbox.com/sh/8t2lxys2tani1m1/AAB2twSh0DQBfNLGUhC8KzsSa?dl=0
-> if anyone asked why I compile two times: this is because I looked in manual and it said
when "Clock Screw detected" make "muliply make command" is one solution
thanks in advance
Robin
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Just Got Here
Threads 1
Posts 2
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| 1:09:48 AM PDT - Thu, Mar 17th 2016 |
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I finally got a exceutable binary with following Installation file, but only if I make "make" two times. Furthermore i got some error messages, which cause maybe troubles. (All files (Installation_6.6, nohup.out, make.log, make2.log, config.log) are again in the same dropbox folders as mentioned in post #1)
Installation file:
#!/bin/sh
source /software/compiler/2015.2.164/bin/compilervars.sh intel64
source /software/compiler/2015.2.164/mkl/bin/mklvars.sh intel64
export PATH=/software/mpi/openmpi_1.10ifort/bin:$PATH
LD_LIBRARY_PATH=/software/compiler/2015.2.164/mkl/lib/intel64/:/software/compiler/2015.2.164/composer_xe_2015/lib/intel64/:/software/compiler/2015.2.164/ga/lib:/usr/lib64:/lib:/lib64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH
export NWCHEM_TOP=/users/robin/NWCHEM/NW_scal/nwchem-6.6
export NWCHEM_TARGET=LINUX64
export NWCHEM_LONG_PATHS=Y
export ARMCI_NETWORK=OPENIB
export TCGRSH=/usr/bin/ssh
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export NWCHEM_MODULES="all"
export USE_NOFSCHECK=TRUE
export LARGE_FILES=TRUE
#export USE_INTERNALBLAS=y
export HAS_BLAS=yes
export USE_SCALAPACK=yes
# Explicit MKL 64 bit
export MKLROOT=/software/compiler/2015.2.164/mkl
export MKLLIB=/software/compiler/2015.2.164/mkl/lib/intel64
export MKLINC=/software/compiler/2015.2.164/mkl/include
export BLASOPT="-L$MKLLIB -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm"
export LAPACK_LIB="-L$MKLLIB -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm"
export BLAS_LIB="-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_openmpi_ilp64 -lpthread -lm"
export SCALAPACK_LIB="-L$MKLLIB -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lmkl_blacs_openmpi_ilp64 -lpthread -lm"
export SCALAPACK_SIZE=8
export BLAS_SIZE=8
export CC=icc
export FC=ifort
echo "cd $NWCHEM_TOP/src"
cd $NWCHEM_TOP/src
echo "BEGIN --- make realclean "
make realclean
echo "END --- make realclean "
echo "BEGIN --- make nwchem_config "
make nwchem_config NWCHEM_MODULES="all"
echo "END --- make nwchem_config "
echo "BEGIN --- make"
make CC=icc FC=ifort FOPTIMIZE="-i8 -I${MKLROOT}/include" > make.log
echo "END --- make "
echo "BEGIN --- make2"
make CC=icc FC=ifort FOPTIMIZE="-i8 -I${MKLROOT}/include" > make2.log
echo "END --- make2 "
1) I have following lines is this concerning to any problem with icc? (in make.log: line 339, 615 and 853)
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from icc object... failed
checking for sysroot... no
and this give the error message: (on the screen or better to say in the nohup.out file)
end of file during read, unit 5, file stdin
2) There seems to be a problem with ARMCI, OPENIB and TCMSG (nohup line: 9475+)
../../ga-5-4/armci/src/xfer/strided.c(1403): warning #167: argument of type "sr_descr_t **" is incompatible with parameter of type "void **"
3) (nohup file line 9531) No rule to make target 'include stamp'. STOP
followed by many *.fh:This statement function has not been uses
4) Then the optimization with BLAS/LPACK/ScaLAPACK begins and give several remarks like (see nohup file line 10019+)
loop was not vectorized: vector dependence
5) Do I need to apply any patches maybe that solve this problems?
following system:
uname -a: Linux n 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
linux distribution: CentOS 6.7
ifort: ifort version 15.0.2
icc: icc version 15.0.2 (gcc version 4.4.7 compatibility)
Even I got all these Problems I get a binary which can be excecuted with mpirun, but I doupt that those problems have no influence on my results. I hope someone have an idea what cause these problems.
Tanks in advance
Robin
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Edited On 1:25:04 AM PDT - Thu, Mar 17th 2016 by Robin1991
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