VENUS/NWChem-6.5 compilation error


Clicked A Few Times
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

Forum Vet
Misha
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
http://nwchemgit.github.io/index.php/Download#Download_the_beta_version_of_the_NWChem_6.6_Re...

Clicked A Few Times
Hi,

Thanks for your help. As you said I downloaded and installed NWChem-6.6 successfully but this time I got another error while compiling the VENUS with NWChem. (The full compiling log is also attached)

/share/apps/nwchem-6.6/lib/LINUX64/libnwctask.a(input_parse.o): In function `input_parse':
/share/apps/nwchem-6.6/src/input/input_parse.F:158: undefined reference to `mm_input_'
/share/apps/nwchem-6.6/lib/LINUX64/libnwctask.a(task_energy.o): In function `task_energy':
/share/apps/nwchem-6.6/src/task/task_energy.F:139: undefined reference to `mm_add_energy_'
/share/apps/nwchem-6.6/lib/LINUX64/libnwctask.a(task_gradient.o): In function `task_gradient':
/share/apps/nwchem-6.6/src/task/task_gradient.F:151: undefined reference to `mm_add_egrad_'
/share/apps/nwchem-6.6/lib/LINUX64/libnwdft.a(dft_input.o): In function `dft_input':
/share/apps/nwchem-6.6/src/nwdft/input_dft/dft_input.F:333: undefined reference to `nwxc_input_'
/share/apps/nwchem-6.6/src/nwdft/input_dft/dft_input.F:337: undefined reference to `nwxc_rtdb_store_'
/share/apps/nwchem-6.6/src/nwdft/input_dft/dft_input.F:338: undefined reference to `nwxc_getvals_'
/share/apps/nwchem-6.6/src/nwdft/input_dft/dft_input.F:341: undefined reference to `nwxc_get_cam_'
/share/apps/nwchem-6.6/src/nwdft/input_dft/dft_input.F:121: undefined reference to `nwxc_init_'
/share/apps/nwchem-6.6/lib/LINUX64/libnwdft.a(xc_util.o): In function `xc_chkgrad':
/share/apps/nwchem-6.6/src/nwdft/xc/xc_util.F:49: undefined reference to `nwxc_getvals_'
/share/apps/nwchem-6.6/src/nwdft/xc/xc_util.F:50: undefined reference to `nwxc_getvals_'
/share/apps/nwchem-6.6/lib/LINUX64/libnwdft.a(xc_util.o): In function `xc_gotxc':
/share/apps/nwchem-6.6/src/nwdft/xc/xc_util.F:74: undefined reference to `nwxc_getvals_'
/share/apps/nwchem-6.6/lib/LINUX64/libnwdft.a(xc_util.o): In function `xc_got2nd':
/share/apps/nwchem-6.6/src/nwdft/xc/xc_util.F:170: undefined reference to `nwxc_getvals_'
/share/apps/nwchem-6.6/lib/LINUX64/libnwdft.a(xc_util.o): In function `xc_chktau':
/share/apps/nwchem-6.6/src/nwdft/xc/xc_util.F:208: undefined reference to `nwxc_getvals_'
/share/apps/nwchem-6.6/lib/LINUX64/libnwdft.a(xc_util.o):/share/apps/nwchem-6.6/src/nwdft/xc/xc_util.F:250: more undefined references to `nwxc_getvals_' follow
/share/apps/nwchem-6.6/lib/LINUX64/libnwdft.a(xc_vdw_main.o): In function `xc_vdw_':


venus_nwchem_log2

Forum Vet
Please try the following

export NWCHEM_MODULES="geninterface nwdft nwxc solvation"
cd $NWCHEM_TOP/src
make nwchem_config
cd util
make FC=ifort
cd ../nwxc
make FC=ifort
cd ..
make FC=ifort link

This will not fix all your problems, since the following error will still occure
./../ga-5-4/armci/src/devices/openib/openib.c:(.text+0x1fbb): undefined reference to `ibv_reg_mr'

In order to fix this, please upload

$NWCHEM_TOP/src/tools/build/config.log
$NWCHEM_TOP/src/tools/build/armci/config.log

Clicked A Few Times
Hi,

I added your given lines exactly to my build script. But this time I got a problem with compiling NWChem.
It seems there is problem with compiling nwxc, and build. Should I add "all" to the NWCHEM_MODULES??

cat: /share/apps/nwchem-6.6/src/tools/build/config.h: No such file or directory
make[1]: Entering directory `/share/apps/nwchem-6.6/src/nwxc'
ifort  -c -i8 -align -fpp -vec-report6 -fimf-arch-consistency=true -finline-limit=250 -O3  -unroll  -ip -xHost -I. -I./nwad -I/share/apps/nwchem-6.6/src/include -I/share/apps/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DIFCV8 -DIFCLINUX -DPARALLEL_DIAG   nwxc.F
nwad.F(619): #error: can't find include file: inp.fh
nwxc_eval.F(305): #error: can't find include file: mafdecls.fh
nwxc_eval.F(1838): #error: can't find include file: mafdecls.fh
nwxc_eval.F(3579): #error: can't find include file: mafdecls.fh
make[1]: *** [/share/apps/nwchem-6.6/lib/LINUX64/libnwxc.a(nwxc.o)] Error 4
make[1]: Leaving directory `/share/apps/nwchem-6.6/src/nwxc'
make: *** [optimized] Error 2
cat: /share/apps/nwchem-6.6/src/tools/build/config.h: No such file or directory
grep: /share/apps/nwchem-6.6/src/tools/build/Makefile: No such file or directory
grep: /share/apps/nwchem-6.6/src/tools/build/Makefile: No such file or directory
grep: /share/apps/nwchem-6.6/src/tools/build/comex/Makefile: No such file or directory
make nwchem.o stubs.o
cat: /share/apps/nwchem-6.6/src/tools/build/config.h: No such file or directory
make[1]: Entering directory `/share/apps/nwchem-6.6/src'
ifort -i8 -align -fpp -vec-report6 -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source  -I.  -I/share/apps/nwchem-6.6/src/include -I/share/apps/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DIFCV8 -DIFCLINUX -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/share/apps/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'"  -c -o nwchem.o nwchem.F
nwchem.F(4): #error: can't find include file: mafdecls.fh
nwchem.F(5): #error: can't find include file: global.fh
nwchem.F(6): #error: can't find include file: rtdb.fh
nwchem.F(7): #error: can't find include file: tcgmsg.fh
nwchem.F(8): #error: can't find include file: pstat.fh
nwchem.F(10): #error: can't find include file: inp.fh
nwchem.F(373): #error: can't find include file: global.fh
nwchem.F(374): #error: can't find include file: inp.fh
nwchem.F(375): #error: can't find include file: mafdecls.fh
nwchem.F(630): #error: can't find include file: global.fh
nwchem.F(632): #error: can't find include file: inp.fh
nwchem.F(633): #error: can't find include file: mafdecls.fh
nwchem.F(634): #error: can't find include file: rtdb.fh
make[1]: *** [nwchem.o] Error 13
make[1]: Leaving directory `/share/apps/nwchem-6.6/src'
make: *** [link] Error 2
Done Making Nwchem

Forum Vet
Misha
This is all I can do to help you.
Cheers


Forum >> NWChem's corner >> Compiling NWChem