Error Message from Task 0:: No such file or directory


Jump to page 1Prev 16
Forum Vet
8:49:59 AM PDT - Tue, Sep 23rd 2014
Please do the following
unset USE_SCALAPACK
unset SCALAPACK
unset SCALAPACK_LIBS
cd $NWCHEM_TOP/src/tools
rm -rf build install
make
cd ..
make link

Clicked A Few Times
4:36:21 AM PDT - Thu, Sep 25th 2014
again failed with the below error:

gfortran -Wl,--export-dynamic -L/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64 -L/opt/ZIP/nwchem-6.3_gnu//src/tools/install/lib -o /opt/ZIP/nwchem-6.3_gnu//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 -lnwxc -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -lnwpython -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil /usr//lib64/python2.6/config/libpython2.6.so -l64to32 -llapack -lblas -L/app1/centos6.3/gnu/mvapich2-1.9/lib -lmpichf90 -Wl,-rpath -Wl,/app1/centos6.3/gnu/mvapich2-1.9/lib -lmpich -lopa -lmpl -libmad -lrdmacm -libumad -libverbs -ldl -lrt -lm -lpthread -lnwcutil -lpthread -lutil -ldl

/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libmp2.a(mp2_make_nos.o): In function `mp2_make_nos_':
mp2_make_nos.F:(.text+0x3d1): undefined reference to `ga_pdsyev_'
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libnwdft.a(dft_main0d.o): In function `dft_main0d_':
dft_main0d.F:(.text+0x10a): undefined reference to `slexit_'
dft_main0d.F:(.text+0x111): undefined reference to `slexit2_'
dft_main0d.F:(.text+0xb54): undefined reference to `ga_cholesky_'
dft_main0d.F:(.text+0xb7e): undefined reference to `ga_llt_i_'
dft_main0d.F:(.text+0x2e32): undefined reference to `ga_llt_i_'
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libnwdft.a(dft_diagn.o): In function `dft_scaleig_':
dft_diagn.F:(.text+0x17c): undefined reference to `ga_pdsyevr_'
dft_diagn.F:(.text+0x1f0): undefined reference to `ga_pdsyev_'
dft_diagn.F:(.text+0x208): undefined reference to `ga_pdsyevx_'
dft_diagn.F:(.text+0x220): undefined reference to `ga_pdsyevd_'
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libnwdft.a(dft_diagn.o): In function `dft_scaleig_so_':
dft_diagn.F:(.text+0xc20): undefined reference to `ga_pzheevr_'
dft_diagn.F:(.text+0xcb8): undefined reference to `ga_pzheevd_'
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libnwdft.a(rt_tddft_init_coulcdfit.o): In function `rt_tddft_init_coulcdfit_':
rt_tddft_init_coulcdfit.F:(.text+0x25a): undefined reference to `ga_cholesky_'
rt_tddft_init_coulcdfit.F:(.text+0x286): undefined reference to `ga_llt_i_'
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libddscf.a(rhf_dens_mo.o): In function `rhf_dens_to_mo_':
rhf_dens_mo.F:(.text+0x440): undefined reference to `ga_pdsyev_'
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libddscf.a(scf_lindep.o): In function `scf_lindep_':
scf_lindep.F:(.text+0x110): undefined reference to `ga_pdsyev_'
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libddscf.a(rohf_canon.o): In function `rohf_canon_sub0_':
rohf_canon.F:(.text+0x35f): undefined reference to `ga_pdsyev_'
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libddscf.a(rohf_canon.o): In function `rohf_canon_':
rohf_canon.F:(.text+0x1272): undefined reference to `ga_pdsyev_'
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libddscf.a(uhf.o): In function `uhf_canon_':
uhf.F:(.text+0x1df2): undefined reference to `ga_pdsyev_'
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libddscf.a(rohf_diis.o):rohf_diis.F:(.text+0x96d): more undefined references to `ga_pdsyev_' follow
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libddscf.a(rohf_diis.o): In function `rohf_diis_solve_':
rohf_diis.F:(.text+0xe57): undefined reference to `ga_pdsygv_'
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libnwcutil.a(ga_matpow.o): In function `ga_matpow_':
ga_matpow.F:(.text+0x172): undefined reference to `ga_pdsyev_'
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libnwints.a(int_1edk_ga.o): In function `int_1edk_ga_':
int_1edk_ga.F:(.text+0x257): undefined reference to `ga_cholesky_'
int_1edk_ga.F:(.text+0x270): undefined reference to `ga_llt_i_'
int_1edk_ga.F:(.text+0x289): undefined reference to `ga_cholesky_'
int_1edk_ga.F:(.text+0x341): undefined reference to `ga_pdsyev_'

Forum Vet
9:22:20 AM PDT - Thu, Sep 25th 2014
OK
There are still the leftovers of the Scalapack defines. Please do the following
cd $NWCHEM_TOP/src/NWints/dk
touch `egrep -l SCALA *F`
cd ../../nwdft
make
touch `egrep -l SCALA */*F`
make
cd ../ddscf
touch `egrep -l SCALA *F`
make
cd ../util
touch `egrep -l SCALA *F`
make
cd ../mp2_grad
touch `egrep -l SCALA *F`
make
cd ..
make link

Clicked A Few Times
12:22:07 AM PDT - Fri, Sep 26th 2014
Issue again:

gfortran -m64 -ffast-math -fdefault-integer-8 -Warray-bounds -O2 -g -fno-aggressive-loop-optimizations -I. -I/opt/ZIP/nwchem-6.3_gnu//src/include -I/opt/ZIP/nwchem-6.3_gnu//src/tools/install/include -DGFORTRAN -DEXT_INT -DLINUX -DLINUX64 -DCHKUNDFLW -DGCC4 -DGCC46 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/opt/ZIP/nwchem-6.3_gnu/'" -DNWCHEM_BRANCH="'6.3'" -c -o nwchem.o nwchem.F
gfortran -m64 -ffast-math -fdefault-integer-8 -Warray-bounds -O2 -g -fno-aggressive-loop-optimizations -I. -I/opt/ZIP/nwchem-6.3_gnu//src/include -I/opt/ZIP/nwchem-6.3_gnu//src/tools/install/include -DGFORTRAN -DEXT_INT -DLINUX -DLINUX64 -DCHKUNDFLW -DGCC4 -DGCC46 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/opt/ZIP/nwchem-6.3_gnu/'" -DNWCHEM_BRANCH="'6.3'" -c -o stubs.o stubs.F
gfortran -Wl,--export-dynamic -L/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64 -L/opt/ZIP/nwchem-6.3_gnu//src/tools/install/lib -o /opt/ZIP/nwchem-6.3_gnu//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 -lnwxc -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -lnwpython -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil /usr//lib64/python2.6/config/libpython2.6.so -l64to32 -llapack -lblas -L/app1/centos6.3/gnu/mvapich2-1.9/lib -lmpichf90 -Wl,-rpath -Wl,/app1/centos6.3/gnu/mvapich2-1.9/lib -lmpich -lopa -lmpl -libmad -lrdmacm -libumad -libverbs -ldl -lrt -lm -lpthread -lnwcutil -lpthread -lutil -ldl
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libnwints.a(int_1edk_ga.o): In function `int_1edk_ga_':
int_1edk_ga.F:(.text+0x257): undefined reference to `ga_cholesky_'
int_1edk_ga.F:(.text+0x270): undefined reference to `ga_llt_i_'
int_1edk_ga.F:(.text+0x289): undefined reference to `ga_cholesky_'
int_1edk_ga.F:(.text+0x341): undefined reference to `ga_pdsyev_'
/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64/libnwints.a(int_1edkso_ga.o): In function `int_1edk_so_ga_':
int_1edkso_ga.F:(.text+0x1fc): undefined reference to `ga_cholesky_'
int_1edkso_ga.F:(.text+0x21e): undefined reference to `ga_llt_i_'
int_1edkso_ga.F:(.text+0x240): undefined reference to `ga_cholesky_'
int_1edkso_ga.F:(.text+0x301): undefined reference to `ga_pdsyev_'
collect2: error: ld returned 1 exit status
make: *** [link] Error 1


This is the code I used:

unset USE_SCALAPACK
unset SCALAPACK
unset SCALAPACK_LIBS
cd $NWCHEM_TOP/src/tools
rm -rf build install
make
cd ..
cd $NWCHEM_TOP/src/NWints/dk
touch `egrep -l SCALA *F`
cd ../../nwdft
make
touch `egrep -l SCALA */*F`
make
cd ../ddscf
touch `egrep -l SCALA *F`
make
cd ../util
touch `egrep -l SCALA *F`
make
cd ../mp2_grad
touch `egrep -l SCALA *F`
make
cd ..
make link

Forum Vet
9:05:56 AM PDT - Fri, Sep 26th 2014
My bad
I have missed one "make" command.
Please try the following (should be pretty quick ...)

unset USE_SCALAPACK
unset SCALAPACK
unset SCALAPACK_LIBS

cd $NWCHEM_TOP/src/NWints/dk
touch `egrep -l SCALA *F`
make
cd ../..
make link

Clicked A Few Times
10:07:11 AM PDT - Fri, Sep 26th 2014
it's successful now. please find the below output:

ldd /app1/centos6.3/gnu/apps/NWChem/bin/nwchem
       linux-vdso.so.1 =>  (0x00007fffcf3ed000)

       libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x00002b34db3d3000)

       libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003f3c400000)

       libgfortran.so.3 => /app1/centos6.3/gnu/gcc-4.8.2/lib64/libgfortran.so.3 (0x00002b34db792000)

       libm.so.6 => /lib64/libm.so.6 (0x0000003f3b800000)

       libmpichf90.so.10 => /app1/centos6.3/gnu/mvapich2-1.9/lib/libmpichf90.so.10 (0x00002b34dbbc1000)

       libmpich.so.10 => /app1/centos6.3/gnu/mvapich2-1.9/lib/libmpich.so.10 (0x00002b34dbdc3000)

       libopa.so.1 => /app1/centos6.3/gnu/mvapich2-1.9/lib/libopa.so.1 (0x00002b34dc315000)

       libmpl.so.1 => /app1/centos6.3/gnu/mvapich2-1.9/lib/libmpl.so.1 (0x00002b34dc516000)

       libibmad.so.5 => /usr/lib64/libibmad.so.5 (0x00002b34dc71a000)

       librdmacm.so.1 => /usr/lib64/librdmacm.so.1 (0x0000003f3d000000)

       libibumad.so.3 => /usr/lib64/libibumad.so.3 (0x0000003f3cc00000)

       libibverbs.so.1 => /usr/lib64/libibverbs.so.1 (0x0000003f3c800000)

       libdl.so.2 => /lib64/libdl.so.2 (0x0000003f3c000000)

       librt.so.1 => /lib64/librt.so.1 (0x00002b34dc933000)

       libutil.so.1 => /lib64/libutil.so.1 (0x0000003f3e800000)

       libgcc_s.so.1 => /app1/centos6.3/gnu/gcc-4.8.2/lib64/libgcc_s.so.1 (0x00002b34dcb3c000)

       libquadmath.so.0 => /app1/centos6.3/gnu/gcc-4.8.2/lib64/libquadmath.so.0 (0x00002b34dcd53000)

       libc.so.6 => /lib64/libc.so.6 (0x0000003f3bc00000)

       /lib64/ld-linux-x86-64.so.2 (0x0000003f3b400000)

Clicked A Few Times
10:12:29 AM PDT - Fri, Sep 26th 2014
segmentation fault still occurs:

gdb nwchem
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-56.el6)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /nfs/app1/centos6.3/gnu/apps/NWChem/bin/nwchem...done.
(gdb) break exit
Breakpoint 1 at 0x51ade8
(gdb) r testnw2
Starting program: /nfs/app1/centos6.3/gnu/apps/NWChem/bin/nwchem testnw2
Error in re-setting breakpoint 1: Cannot access memory at address 0x51ade8
Error in re-setting breakpoint 1: Cannot access memory at address 0x51ade8
Error in re-setting breakpoint 1: Cannot access memory at address 0x51ade8
process 15294 is executing new program: /nfs/app1/centos6.3/gnu/apps/NWChem/bin/nwchem
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.80.el6.x86_64
[Thread debugging using libthread_db enabled]
warning: the debug information found in "/usr/lib/debug//usr/lib64/libipathverbs-rdmav2.so.debug" does not match "/usr/lib64/libipathverbs-rdmav2.so" (CRC mismatch).

warning: the debug information found in "/usr/lib/debug/usr/lib64/libipathverbs-rdmav2.so.debug" does not match "/usr/lib64/libipathverbs-rdmav2.so" (CRC mismatch).

warning: the debug information found in "/usr/lib/debug//usr/lib64/libmthca-rdmav2.so.debug" does not match "/usr/lib64/libmthca-rdmav2.so" (CRC mismatch).

warning: the debug information found in "/usr/lib/debug/usr/lib64/libmthca-rdmav2.so.debug" does not match "/usr/lib64/libmthca-rdmav2.so" (CRC mismatch).

argument  1 = testnw2

 Unable to open testnw2 --- appending .nw






             Northwest Computational Chemistry Package (NWChem) 6.3

             ------------------------------------------------------




                   Environmental Molecular Sciences Laboratory

                      Pacific Northwest National Laboratory

                               Richland, WA 99352



                             Copyright (c) 1994-2012

                      Pacific Northwest National Laboratory

                           Battelle Memorial Institute



            NWChem is an open-source computational chemistry package

                       distributed under the terms of the

                     Educational Community License (ECL) 2.0

            A copy of the license is included with this distribution

                             in the LICENSE.TXT file



                                 ACKNOWLEDGMENT

                                 --------------



           This software and its documentation were developed at the

           EMSL at Pacific Northwest National Laboratory, a multiprogram

           national laboratory, operated for the U.S. Department of Energy

           by Battelle under Contract Number DE-AC05-76RL01830. Support

           for this work was provided by the Department of Energy Office

           of Biological and Environmental Research, Office of Basic

           Energy Sciences, and the Office of Advanced Scientific Computing.

Clicked A Few Times
10:12:41 AM PDT - Fri, Sep 26th 2014
Job information
          ---------------

   hostname        = atlas5-c01

   program         = /nfs/app1/centos6.3/gnu/apps/NWChem/bin/nwchem

   date            = Sat Sep 27 01:10:31 2014



   compiled        = Thu_Sep_11_09:59:58_2014

   source          = /opt/ZIP/nwchem-6.3/

   nwchem branch   = 6.3

   nwchem revision = 24652

   ga revision     = 10379

   input           = testnw2.nw

   prefix          = feco5.

   data base       = ./feco5.db

   status          = startup

   nproc           =        1

   time left       =     -1s

   batch job id    = 182048



          Memory information

          ------------------



   heap     =   13107201 doubles =    100.0 Mbytes

   stack    =   13107201 doubles =    100.0 Mbytes

   global   =   26214400 doubles =    200.0 Mbytes (distinct from heap & stack)

   total    =   52428802 doubles =    400.0 Mbytes

   verify   = yes

   hardfail = no




          Directory information

          ---------------------



 0 permanent = .

 0 scratch   = .






                               NWChem Input Module

                               -------------------



Program received signal SIGSEGV, Segmentation fault.
0x0000000002b69766 in LSteps_Any_Loop4gas_1 ()
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.80.el6.x86_64 libipathverbs-1.2-4.el6.x86_64 libmthca-1.0.6-3.el6.x86_64 python-libs-2.6.6-29.el6_2.2.x86_64
(gdb) where
  1. 0 0x0000000002b69766 in LSteps_Any_Loop4gas_1 ()
  2. 1 0x0000000004aa2260 in cgeometry_ ()
  3. 2 0x00007fffffffc580 in ?? ()
  4. 3 0x0000000000000000 in ?? ()

Forum Vet
10:42:36 AM PDT - Fri, Sep 26th 2014
Please send me the complete output of the following commands

1) unset BLASOPT; make link

2) nm $NWCHEM_TOP/bin/LINUX64/nwchem | grep -i mkl | grep -i dgemm| grep T

3) nm `which nwchem` | grep -i mkl | grep -i dgemm| grep T

4) which nwchem

Clicked A Few Times
11:01:27 AM PDT - Fri, Sep 26th 2014
unset BLASOPT; make link
make nwchem.o stubs.o
make[1]: warning: -jN forced in submake: disabling jobserver mode.
gfortran -m64 -ffast-math -fdefault-integer-8 -Warray-bounds -O2 -g -fno-aggressive-loop-optimizations -I. -I/opt/ZIP/nwchem-6.3_gnu//src/include -I/opt/ZIP/nwchem-6.3_gnu//src/tools/install/include -DGFORTRAN -DEXT_INT -DLINUX -DLINUX64 -DCHKUNDFLW -DGCC4 -DGCC46 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/opt/ZIP/nwchem-6.3_gnu/'" -DNWCHEM_BRANCH="'6.3'" -c -o nwchem.o nwchem.F
gfortran -m64 -ffast-math -fdefault-integer-8 -Warray-bounds -O2 -g -fno-aggressive-loop-optimizations -I. -I/opt/ZIP/nwchem-6.3_gnu//src/include -I/opt/ZIP/nwchem-6.3_gnu//src/tools/install/include -DGFORTRAN -DEXT_INT -DLINUX -DLINUX64 -DCHKUNDFLW -DGCC4 -DGCC46 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/opt/ZIP/nwchem-6.3_gnu/'" -DNWCHEM_BRANCH="'6.3'" -c -o stubs.o stubs.F
gfortran -Wl,--export-dynamic -L/opt/ZIP/nwchem-6.3_gnu//lib/LINUX64 -L/opt/ZIP/nwchem-6.3_gnu//src/tools/install/lib -o /opt/ZIP/nwchem-6.3_gnu//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 -lnwxc -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -lnwpython -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil /usr//lib64/python2.6/config/libpython2.6.so -l64to32 -llapack -lblas -L/app1/centos6.3/gnu/mvapich2-1.9/lib -lmpichf90 -Wl,-rpath -Wl,/app1/centos6.3/gnu/mvapich2-1.9/lib -lmpich -lopa -lmpl -libmad -lrdmacm -libumad -libverbs -ldl -lrt -lm -lpthread -lnwcutil -lpthread -lutil -ldl

which nwchem
/opt/ZIP/nwchem-6.3_gnu/bin/LINUX64/nwchem

no output for nm commands

Forum Vet
11:24:58 AM PDT - Fri, Sep 26th 2014
NWCHEM_TOP discrepancy
I see from your link command that
NWCHEM_TOP=/opt/ZIP/nwchem-6.3_gnu
while your output file shows
NWCHEM_TOP=/opt/ZIP/nwchem-6.3/
(you can spot this from the line
source = /opt/ZIP/nwchem-6.3/
)

One more indication that you have been not running the NWChem binary that you have just created is the output line

program = /nfs/app1/centos6.3/gnu/apps/NWChem/bin/nwchem

The line should read, instead

program = /opt/ZIP/nwchem-6.3_gnu/bin/LINUX64/nwchem

You might want to have a look at the scripts/environment you use to run NWChem to be sure that you do use
/opt/ZIP/nwchem-6.3_gnu/bin/LINUX64/nwchem

Clicked A Few Times
9:53:39 PM PDT - Mon, Oct 6th 2014
sorry for the delay.

Finally I could run successfully after compiling and running from the same location i.e. /nfs/app1/centos6.3/gnu/apps/NWChem

I read some where that once the binaries are compiled, I can move to my desired location and run from there, hence I was compiling from /opt/ZIP/nwchem-6.3_gnu/ however this method never worked for me.

Thanks for all the assistance provided to me for the troubleshooting.


Forum >> NWChem's corner >> Running NWChem
Jump to page 1Prev 16