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| 7:05:22 AM PDT - Fri, Oct 2nd 2015 |
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Hi,
I'm trying to compile VENUS by NWChem 6.5 with OpenMPI 1.10, and Intel Compiler on infiniband network, and external GA compiled for ib.
Here is the script that I'm running to make and build the software packages:
#!/bin/bash
source /opt/intel/composer_xe_2013_sp1.3.174/bin/compilervars.sh intel64
export MPI_LOC=/opt/openmpi_intel_ib
export GA=/share/apps/GA/ga-5-3_intel_ib
export PATH=${MPI_LOC}/bin/:$PATH
export LD_LIBRARY_PATH=$MPI_LOC/lib/openmpi:$MPI_LOC/lib:$GA/lib:$LD_LIBRARY_PATH
#
export NWCHEM_TOP=./nwchem-6.5-ib
export TCGRSH=/usr/bin/ssh
export NWCHEM_TARGET=LINUX64
export USE_NOFSCHECK=Y
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LIB=$MPI_LOC/lib
export MPI_INCLUDE=$MPI_LOC/include
export NWCHEM_MPIF_WRAP=$MPI_LOC/bin/mpifort
export NWCHEM_MPIC_WRAP=$MPI_LOC/bin/mpicc
export NWCHEM_MPICXX_WRAP=$MPI_LOC/bin/mpicxx
#
# USE -lmpi_mpifh -lmpi_usempif08 INSTEAD OF -lmpi_f90 -lmpi_f77 IN OPENMPI 1.10
#
export LIBMPI="-lmpi_mpifh -lmpi_usempif08 -lmpi -ldl -Wl,--export-dynamic -lnsl -lutil"
export ARMCI_NETWORK=OPENIB
export IB_HOME=/usr
export IB_INCLUDE=$IB_HOME/include
export IB_LIB=$IB_HOME/lib64
export IB_LIB_NAME="-larmci -lrdmacm -libverbs -libumad -lpthread"
export LARGE_FILES=y
export PYTHON_EXE=/usr/bin/python
export PYTHONVERSION=2.6
export USE_PYTHON64=yes
export PYTHONPATH=/usr/lib64/python2.6/site-packages/
export PYTHONHOME=/usr
export PYTHONLIBTYPE=a
export NWCHEM_MODULES="all qm geninterface"
export FC=ifort
export CC=icc
export CXX=icpc
#
cd src
#make realclean
make clean
#
make nwchem_config NWCHEM_MODULES=venus
make nwchem_config
make CC=icc FC=ifort CXX=icpc 2>&1 | tee ../make.log
echo "Done Making Nwchem"
echo "proceeding to build Venus . DO you want to do that?"
read response
#
rm -f stubs.o
make stubs.o 2>&1 | tee ../make1.log
#
cd ../venus-nwchem-april2013
make clean
make FC=ifort CC=icc CXX=icpc 2>&1 | tee -a ../make1.log
This scripts compiles the NWChem, and "stubs.o" successfully with no error. However, in case of
compiling the VENUS, it causes error as below (I made the used libraries bold to let you see the libs
using in VENUS):
...
...
ifort -i8 -align -vec-report6 -fimf-arch-consistency=true -O2 -g -fp-model source ADAMSM.o ANGVEL.o AXT.o BAREXC.o CENMAS.o CUBEND.o DANGLE.o DMBE.o DVDQ.o EBOND.o EIGN.o EIGOUT.o ENERGY.o ENMODE.o vFDATE.o FGMTRX.o FINAL.o FINLNJ.o FMTRX.o GAMA.o GFINAL.o MPATHO.o GHOST.o GINROT.o GLPAR.o GPATH.o GRCONV.o GWRITE.o HALPHA.o HBEND.o HEXP.o HFD.o HNONB.o HOMOQP.o HTAU.o INITEBK.o INITQP.o LENJ.o LEPS1.o LEPS2.o LMEXCT.o LMODE.o MORSE.o MPATH.o NMODE.o ORTHAN.o PARSN2.o PARTI.o POTEN.o RAND0.o RAND1.o RANDST.o READPT.o RELAX.o ROTATE.o ROTEN.o ROTN.o RUNGEK.o RYDBG.o SELECT.o STRET.o SURF.o SYBMOL.o TEST.o TETRA.o THRMAN.o VENUS.o VRR.o VRT.o VSN2.o VTT.o WEBOND.o WENMOD.o WLBOND.o STATPT.o HEIGHT.o CPUSEC.o RADAU.o SYMPLE.o lnb.o thermo.o thermbath.o gasdev.o CRCO6.o POTENZ.o hessint.o verlet.o JMAXCALC.o PROBJ.o QMCALC.o NWCHEM_LINK.o -L/share/apps/nwchem-6.5-ib/lib/LINUX64 -L/share/apps/nwchem-6.5-ib/src/tools/install/lib -L/opt/openmpi_intel_ib/lib -o ven_nw.e /share/apps/nwchem-6.5-ib/src/stubs.o -lgeninterface -lnwcutil -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 -lsolvation -lbq -lnwcutil -llapack -lblas -larmci -lmpi_mpifh -lmpi_usempif08 -lmpi -ldl -Wl,--export-dynamic -lnsl -lutil
/share/apps/nwchem-6.5-ib/lib/LINUX64/libnwpw.a(nwpw_input.o): In function `nwpw_input':
/share/apps/nwchem-6.5-ib/src/nwpw/nwpw_input.F:626: undefined reference to `nwxc_input_'
/share/apps/nwchem-6.5-ib/src/nwpw/nwpw_input.F:630: undefined reference to `nwxc_rtdb_store_'
/share/apps/nwchem-6.5-ib/src/nwpw/nwpw_input.F:635: undefined reference to `nwxc_has_hfx_'
/share/apps/nwchem-6.5-ib/src/nwpw/nwpw_input.F:642: undefined reference to `nwxc_wght_hfx_'
/share/apps/nwchem-6.5-ib/src/nwpw/nwpw_input.F:645: undefined reference to `nwxc_wght_hfx_'
/share/apps/nwchem-6.5-ib/src/nwpw/nwpw_input.F:652: undefined reference to `nwxc_has_cam_'
/share/apps/nwchem-6.5-ib/src/nwpw/nwpw_input.F:673: undefined reference to `nwxc_rtdb_delete_'
/share/apps/nwchem-6.5-ib/src/nwpw/nwpw_input.F:653: undefined reference to `nwxc_get_cam_'
/share/apps/nwchem-6.5-ib/lib/LINUX64/libpaw.a(paw_gga.o): In function `paw_gga_':
paw_gga.F:(.text+0x1f3): undefined reference to `nwxc_is_on_'
paw_gga.F:(.text+0x2d7): undefined reference to `nwxc_is_on_'
paw_gga.F:(.text+0x48b): undefined reference to `nwxc_eval_df_'
paw_gga.F:(.text+0x6d1): undefined reference to `nwxc_eval_df_'
/share/apps/nwchem-6.5-ib/lib/LINUX64/libpaw.a(paw_electron.o): In function `paw_electron_run_':
paw_electron.F:(.text+0x88d): undefined reference to `nwxc_is_on_'
paw_electron.F:(.text+0x897): undefined reference to `nwxc_is_on_'
paw_electron.F:(.text+0x8a1): undefined reference to `nwxc_is_lda_'
/share/apps/nwchem-6.5-ib/lib/LINUX64/libpaw.a(paw_electron.o): In function `paw_electron_gen_scf_potentials_':
paw_electron.F:(.text+0x10fe): undefined reference to `nwxc_is_on_'
paw_electron.F:(.text+0x1108): undefined reference to `nwxc_is_on_'
paw_electron.F:(.text+0x1112): undefined reference to `nwxc_is_lda_'
/share/apps/nwchem-6.5-ib/lib/LINUX64/libpspw.a(v_bwexc_all.o): In function `v_bwexc_all_':
v_bwexc_all.F:(.text+0x27): undefined reference to `nwxc_is_on_'
v_bwexc_all.F:(.text+0x31): undefined reference to `nwxc_is_on_'
v_bwexc_all.F:(.text+0x3b): undefined reference to `nwxc_is_lda_'
v_bwexc_all.F:(.text+0x12b): undefined reference to `nwxc_is_on_'
v_bwexc_all.F:(.text+0x135): undefined reference to `nwxc_is_on_'
v_bwexc_all.F:(.text+0x13f): undefined reference to `nwxc_is_gga_'
v_bwexc_all.F:(.text+0x19c): undefined reference to `nwxc_is_mgga_'
/share/apps/nwchem-6.5-ib/lib/LINUX64/libpspw.a(v_bwexc_all.o): In function `v_bwexc_all_tmp1_':
v_bwexc_all.F:(.text+0x306): undefined reference to `nwxc_is_on_'
v_bwexc_all.F:(.text+0x310): undefined reference to `nwxc_is_on_'
v_bwexc_all.F:(.text+0x31a): undefined reference to `nwxc_is_lda_'
v_bwexc_all.F:(.text+0x36d): undefined reference to `nwxc_is_on_'
v_bwexc_all.F:(.text+0x377): undefined reference to `nwxc_is_on_'
v_bwexc_all.F:(.text+0x381): undefined reference to `nwxc_is_gga_'
/share/apps/nwchem-6.5-ib/lib/LINUX64/libpspw.a(v_bwexc_all.o): In function `v_bwexc_print_':
v_bwexc_all.F:(.text+0x4f4): undefined reference to `nwxc_is_on_'
v_bwexc_all.F:(.text+0xb5a): undefined reference to `nwxc_print_nwpw_'
/share/apps/nwchem-6.5-ib/lib/LINUX64/libpspw.a(v_exc.o): In function `vxc_':
v_exc.F:(.text+0x86): undefined reference to `nwxc_is_on_'
v_exc.F:(.text+0x138): undefined reference to `nwxc_is_on_'
v_exc.F:(.text+0x135a): undefined reference to `nwxc_eval_df_'
/share/apps/nwchem-6.5-ib/lib/LINUX64/libpspw.a(v_mexc.o): In function `v_mexc_':
v_mexc.F:(.text+0xd2f): undefined reference to `nwxc_eval_df_'
v_mexc.F:(.text+0x2045): undefined reference to `nwxc_eval_df_'
/share/apps/nwchem-6.5-ib/lib/LINUX64/libpspw.a(v_bwexc.o): In function `v_bwexc_':
v_bwexc.F:(.text+0xb6e): undefined reference to `nwxc_is_on_'
v_bwexc.F:(.text+0x1a00): undefined reference to `nwxc_eval_df_'
v_bwexc.F:(.text+0x2200): undefined reference to `nwxc_is_on_'
v_bwexc.F:(.text+0x2276): undefined reference to `nwxc_eval_df_'
...
...
Was there any changes in libraries (Specially in geninterface module) or this is the problem from GA?
Here is the link to full installation process log:
venus_nwchem.log
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