VENUS/NWChem-6.5 compilation error

From NWChem

Viewed 35 times, With a total of 1 Posts
Jump to: navigation, search

Just Got Here
Threads 1
Posts 1

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:

source  /opt/intel/composer_xe_2013_sp1.3.174/bin/ 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 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=$MPI_LOC/bin/mpicxx
# USE -lmpi_mpifh -lmpi_usempif08 INSTEAD OF -lmpi_f90 -lmpi_f77 IN OPENMPI 1.10
export LIBMPI="-lmpi_mpifh -lmpi_usempif08 -lmpi -ldl -Wl,--export-dynamic -lnsl -lutil"
export IB_HOME=/usr
export IB_INCLUDE=$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 USE_PYTHON64=yes
export PYTHONPATH=/usr/lib64/python2.6/site-packages/
export PYTHONHOME=/usr
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:

Forum Vet
Threads 4
Posts 933
Could you please switch to NWChem 6.6 since the nwxc integrations has been improved.
I have justed tested and verified that generating a module with NWCHEM_MODULES="geninterface nwdft solvation" works.

6.6 details at

Forum >> NWChem's corner >> Compiling NWChem

Who's here now Members 0 Guests 1 Bots/Crawler 0

AWC's: 2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC