moints semi: failed to open half int file


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Forum Vet
3:00:49 PM PDT - Thu, Aug 2nd 2012
Output file from run on Cray XE6
Ysun
You can download the output from a successful run of your input file on the Cray XE6 at the ORNL OLCF
at the followin URL

http://users.nccs.gov/~apra/mp2.out

Clicked A Few Times
8:27:10 AM PDT - Fri, Aug 3rd 2012
Hi Edoapra,

I have added the memory directive and removed scratchdisk as shown in your output. However the error still appears with NWChem 6.1 and 6.1.1. The compilation instructions of NWChem 6.1 on our system can be found at http://www.hector.ac.uk/support/documentation/software/nwchem/compiling_6-1_phase3.php Is there any problem in the compilation steps for example the use of libraries and environment variables?

Thanks,

Yudong

Forum Vet
9:42:10 AM PDT - Fri, Aug 3rd 2012
Quote:Ysun Aug 3rd 7:27 am
Hi Edoapra,

I have added the memory directive and removed scratchdisk as shown in your output. However the error still appears with NWChem 6.1 and 6.1.1. The compilation instructions of NWChem 6.1 on our system can be found at http://www.hector.ac.uk/support/documentation/software/nwchem/compiling_6-1_phase3.php Is there any problem in the compilation steps for example the use of libraries and environment variables?

Thanks,

Yudong


Yudong

For the 6.1.1 compilation,

1) the value used for ARMCI_NETWORK=LIBONESIDED should not be used, it should be GEMINI, instead, plus OLD_GA=y should not be set, and -- because of thesechanges -- you do not need to do the following
"In the GNUmakefile files in: src/, src/tools/ change all references from armci-gemini to gemini"

2) what make command was used? The correct one, essential to get your mp2 run to work, is

make FC=ftn

Cheers, Edo

Clicked A Few Times
4:38:56 AM PDT - Mon, Aug 6th 2012
Edo,

Do you mean not changing armci to armci-gemini in GNUmakefiles as required in http://www.hector.ac.uk/support/documentation/software/nwchem/compiling_6-1_phase3.php?

If yes, do I need to copy armci-gemini/, global/, tcgmsg-mpi/ from the GEMINI GA 4.3 to src/tools/?

Thanks,

Ysun

Clicked A Few Times
4:47:41 AM PDT - Mon, Aug 6th 2012
Edo,

If I use the original armci included in nwchem-6.1.1-src/tools, I get an error in make. What's wrong with it?

../ga-5-1/configure --prefix=/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/tools/install --with-tcgmsg --with-mpi --enable-peigs --enable-underscoring --disable-mpi-tests --without-scalapack --without-lapack --with-blas8= --with-gemini CC=cc MPICC=cc F77=ftn MPIF77=ftn
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for TARGET base (64bit-ness checked later)... LINUX
checking whether we think this system is what we call SYSV... yes
checking whether we are cross compiling... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
configure: Detected VPATH build
configure:
configure: C compiler
configure:
checking for style of include used by make... GNU
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... configure: error: in `/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/tools/build':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
make[1]: *** [build/config.status] Error 1
make: *** [libraries] Error 1

Thanks,

Ysun

Forum Vet
9:55:49 AM PDT - Mon, Aug 6th 2012
Quote:Ysun Aug 6th 3:47 am
Edo,

If I use the original armci included in nwchem-6.1.1-src/tools, I get an error in make. What's wrong with it?

.....
checking whether we are cross compiling... configure: error: in `/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/tools/build':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
make[1]: *** [build/config.status] Error 1
make: *** [libraries] Error 1

Thanks,

Ysun


Ysun,
I am getting a similar behaviour on the Cray XE6 at Oak Ridge.
The fix I am using for the ORNL machine is the following:

cd $NWCHEM_TOP/src/tools
module swap xtpe-istanbul xtpe-interlagos
make FC=ftn
module swap xtpe-interlagos xtpe-istanbul
cd ..
make FC=ftn

Let me know if this works for you, too.

Cheers, Edo

Clicked A Few Times
4:21:52 AM PDT - Thu, Aug 9th 2012
Edo,

How do you configure the make? I use 

 make 64_to_32

Then make src/tools with xtpe-istanbul (not xtep-interlagos which causes "can't run C compiled programs" error) and make src/ with xtep-interlagos. However there are errors of undefined libraray functions when making src/.

ftn -L/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64 -L/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/tools/install/lib -i8 -Mdalign -Mllalign -Kieee -o /work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/bin/LINUX64/nwchem nwchem.o stubs.o -lnwctask -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -lpeigs -lperfm -lcons -lbq -lnwcutil -l64to32 -llapack -lblas
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libmp2.a(mp2_make_nos.o): In function `mp2_make_nos_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/mp2_grad/./mp2_make_nos.F:94: undefined reference to `ga_pdsyev_'
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libnwdft.a(dft_main0d.o): In function `dft_main0d_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/nwdft/scf_dft/./dft_main0d.F:99: undefined reference to `slexit_'
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/nwdft/scf_dft/./dft_main0d.F:99: undefined reference to `slexit2_'
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/nwdft/scf_dft/./dft_main0d.F:321: undefined reference to `ga_cholesky_'
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/nwdft/scf_dft/./dft_main0d.F:350: undefined reference to `ga_llt_i_'
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libnwdft.a(dft_diagn.o): In function `dft_scaleig_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/nwdft/scf_dft/./dft_diagn.F:210: undefined reference to `ga_pdsyev_'
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/nwdft/scf_dft/./dft_diagn.F:212: undefined reference to `ga_pdsyevx_'
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/nwdft/scf_dft/./dft_diagn.F:214: undefined reference to `ga_pdsyevd_'
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libddscf.a(rhf_dens_mo.o): In function `rhf_dens_to_mo_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/ddscf/./rhf_dens_mo.F:125: undefined reference to `ga_pdsyev_'
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libddscf.a(scf_lindep.o): In function `scf_lindep_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/ddscf/./scf_lindep.F:49: undefined reference to `ga_pdsyev_'
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libddscf.a(rohf_canon.o): In function `rohf_canon_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/ddscf/./rohf_canon.F:46: undefined reference to `ga_pdsyev_'
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libddscf.a(rohf_canon.o): In function `rohf_canon_sub0_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/ddscf/./rohf_canon.F:209: undefined reference to `ga_pdsyev_'
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libddscf.a(uhf.o): In function `uhf_canon_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/ddscf/./uhf.F:1311: undefined reference to `ga_pdsyev_'
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libddscf.a(rohf_diis.o): In function `rohf_diis_solve_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/ddscf/./rohf_diis.F:190: undefined reference to `ga_pdsygv_'
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libddscf.a(rohf_diis.o): In function `rohf_ao_orthonorm_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/ddscf/./rohf_diis.F:446: undefined reference to `ga_pdsyev_'
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libnwcutil.a(ga_matpow.o): In function `ga_matpow_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/util/./ga_matpow.F:106: undefined reference to `ga_pdsyev_'
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libnwints.a(int_1edk_ga.o): In function `int_1edk_ga_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/NWints/dk/./int_1edk_ga.F:147: undefined reference to `ga_cholesky_'
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/NWints/dk/./int_1edk_ga.F:147: undefined reference to `ga_llt_i_'
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/NWints/dk/./int_1edk_ga.F:147: undefined reference to `ga_cholesky_'
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/NWints/dk/./int_1edk_ga.F:147: undefined reference to `ga_pdsyev_'
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libnwints.a(int_1edkso_ga.o): In function `int_1edk_so_ga_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/NWints/dk/./int_1edkso_ga.F:133: undefined reference to `ga_cholesky_'
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/NWints/dk/./int_1edkso_ga.F:142: undefined reference to `ga_llt_i_'
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/NWints/dk/./int_1edkso_ga.F:145: undefined reference to `ga_cholesky_'
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/NWints/dk/./int_1edkso_ga.F:148: undefined reference to `ga_pdsyev_'
make: *** [all] Error 2

The library paths in the ftn above contain the libraries as below. Is there anything missing?

lib/LINUX64:

lib64to32.a libcons.a libesp.a libmp2.a libofpw.a libpspw.a libtce.a
libanalyze.a libcphf.a libetrans.a libnwctask.a liboptim.a libqhop.a libvib.a
libband.a libdangchang.a libgradients.a libnwcutil.a libpaw.a libqmd.a libvscf.a
libblas.a libddscf.a libguess.a libnwdft.a libpeigs.a libqmmm.a
libbq.a libdntmc.a libhessian.a libnwints.a libperfm.a librimp2.a
libcafe.a libdplot.a liblapack.a libnwmd.a libpfft.a libselci.a
libccca.a libdrdy.a libmcscf.a libnwpw.a libprepar.a libspace.a
libccsd.a libdriver.a libmoints.a libnwpwlib.a libproperty.a libstepper.a

tools/install/lib:

libarmci.a libarmci.la libga.a libga.la

Forum Vet
3:33:50 PM PDT - Thu, Aug 9th 2012
Ysun,
The missing symbol are coming from Scalapack.
The problem is that the Global Arrays shipped with NWChem 6.1 require a variety of env. variable for specifying the Scalapck settings.
This is what I use on the Cray XK6
USE_SCALAPACK=y
SCALAPACK_LIB=-lsci_pgi
SCALAPACK=-lsci_pgi
SCALAPACK_SIZE=4

In order to have the tools digest these new definitions, you need to configure the tools again.
One way to do this is the following:
cd $NWCHEM_TOP/src/tools
rm -rf build
make FC=ftn

Let me know if fixes your problem.

Cheers, Edo


Quote:Ysun Aug 9th 3:21 am
Edo,

How do you configure the make? I use 

 make 64_to_32

Then make src/tools with xtpe-istanbul (not xtep-interlagos which causes "can't run C compiled programs" error) and make src/ with xtep-interlagos. However there are errors of undefined library functions when making src/.

ftn -L/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64 -L/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/tools/install/lib -i8 -Mdalign -Mllalign -Kieee -o /work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/bin/LINUX64/nwchem nwchem.o stubs.o -lnwctask -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -lpeigs -lperfm -lcons -lbq -lnwcutil -l64to32 -llapack -lblas
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libmp2.a(mp2_make_nos.o): In function `mp2_make_nos_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/mp2_grad/./mp2_make_nos.F:94: undefined reference to `ga_pdsyev_'
/work/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/lib/LINUX64/libnwdft.a(dft_main0d.o): In function `dft_main0d_':
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/nwdft/scf_dft/./dft_main0d.F:99: undefined reference to `slexit_'
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/nwdft/scf_dft/./dft_main0d.F:99: undefined reference to `slexit2_'
/esfs2/z03/z03/ydsun/queries/q235816_nwchem/nwchem-6.1.1-src/src/nwdft/scf_dft/./dft_main0d.F:321: undefined reference to `ga_cholesky_'

Clicked A Few Times
4:41:49 AM PDT - Fri, Aug 10th 2012
Edo,

Done. I have got the output with the NWChem 6.1.1.

Many thanks.

Ysun


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