Problems in compiling NWChem

Clicked A Few Times

9:28:05 AM PDT - Thu, Sep 24th 2015
Dear all, I have some problems in compiling NWChem. I get the following error: /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `__svml_idiv4' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_trrealloc' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_trspace' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_trDebugLevel' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `__intel_sse2_strcpy' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_TrSetMaxMem' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `__intel_sse2_strchr' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_trlevel' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `__intel_sse2_strrchr' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_trmalloc' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_env2bool' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `__intel_sse2_strncmp' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_env2range' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `_intel_fast_memset' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_trcalloc' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_trfree' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_env2str' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_trstrdup' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `__intel_sse2_strlen' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_trdump' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `__intel_sse2_strncpy' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `__intel_sse2_strcspn' /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib/libmpich.so: undefined refer ence to `MPL_trinit' collect2: error: ld returned 1 exit status make: *** [all] Error 1 Any idea about which is the problem? Thanks a lot Alessandro

Forum Vet

10:12:18 AM PDT - Thu, Sep 24th 2015
Please post output from the following commands mpif90 -show env \| grep MPI_

Clicked A Few Times

1:02:39 AM PDT - Fri, Sep 25th 2015
Sorry, it seems the command mpif90 -show doesn't work (mpif90, command not found)...

Forum Vet

9:34:24 AM PDT - Fri, Sep 25th 2015
Quote:Alessandro.chiesa Sep 25th 12:02 am Sorry, it seems the command mpif90 -show doesn't work (mpif90, command not found)... Try /usr/local/parastation/mpi2-intel12-mt-5.0.27-1/bin/mpif90 -show

Clicked A Few Times

9:43:28 AM PDT - Fri, Sep 25th 2015
Many thanks, here is the answer ifort -I/usr/local/parastation/mpi2-intel12-mt-5.0.27-1/include -I/usr/local/parastation/mpi2-intel12-mt-5.0.27-1/include -L/usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib -lmpichf90 -lmpichf90 -lmpich -Wl,-rpath-link=/usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib

Forum Vet

10:52:19 AM PDT - Fri, Sep 25th 2015
Please try MPI_INCLUDE=usr/local/parastation/mpi2-intel12-mt-5.0.27-1/include MPI_LIB=" -lmpichf90 -lmpichf90 -lmpich" LIBMPI=/usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib if this does not work, Try to replace the previous MPI_LIB with MPI_LIB="-lmpichf90 -lmpichf90 -lmpich -Wl,-rpath-link=/usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib"

Clicked A Few Times

11:38:17 PM PDT - Sun, Sep 27th 2015
Thank you for the suggestion, I tried both, but unfortunately it doesn't work. Always the same error: "collect2: error: ld returned 1 exit status make: *** [all] Error 1"

Forum Vet

9:36:00 AM PDT - Mon, Sep 28th 2015
Quote:Alessandro.chiesa Sep 27th 10:38 pm Thank you for the suggestion, I tried both, but unfortunately it doesn't work. Always the same error: "collect2: error: ld returned 1 exit status make: *** [all] Error 1" Please copy and paste the last 30 lines of your link step

Clicked A Few Times

10:05:45 AM PDT - Mon, Sep 28th 2015

I am not sure I have understood correctly... anyway, this is my build_nwchem file

 1 #!/bin/bash

 2 #export USE_GPROF=yes

 3 export USE_SUBGROUPS=yes

 4 export USE_MPI=yes

 5 #export OLD_GA=yes

 6 export MSG_COMMS=MPI

 7 export USE_PYTHON64=yes

 8 export MPI_LOC=/usr/local/parastation/mpi2-intel12-mt-5.0.27-1

 9 export MPI_INCLUDE=$MPI_LOC/include

10 export MPI_LIB=$MPI_LOC/lib

11 #export MPI_LIB=" -lmpichf90 -lmpichf90 -lmpich"

12 #export LIBMPI=$MPI_LOC/lib

13 #export LIBMPI="-lfmpich -lmpich -lpthread"        # MPICH2 1.2

14 export LIBMPI="-lmpichf90 -lmpich -lmpl -lpthread" # MPICH2 1.3.1

15 export ARMCI_NETWORK=OPENIB

16 export PYTHONHOME=/usr/bin

17 export PYTHONVERSION=2.6

18 export NWCHEM_TOP=`pwd`

19 export NWCHEM_TARGET=LINUX64

20 export NWCHEM_MODULES="all python"

21 export NWCHEM_MODULES="all"

22 export NWCHEM_EXECUTABLE=$NWCHEM_TOP/bin/LINUX64/nwchem

23 export PYTHONPATH=./:$NWCHEM_TOP/contrib/python/

24 export LARGE_FILES=TRUE

25 export ENABLE_COMPONENT=yes

26 export TCGGRSH=/usr/bin/ssh

27 export FOPTIMIZE="-O3 -xSSE2,SSE3,SSSE3,SSE4.1,SSE4.2 -no-prec-div -funroll-loops -unroll-aggressive"

28 export COPTIMIZE="-O3 -xSSE2,SSE3,SSSE3,SSE4.1,SSE4.2 -no-prec-div -funroll-loops"

30 cd $NWCHEM_TOP/src

31 #make DIAG=PAR FC=gfortran CC=gcc CDEBUG="-g -ffpe-trap=invalid,zero,overflow" FDEBUG="-g -ffpe-trap=invalid,zero,overflow" FOPTIMIZE="-g -ffpe-trap=invalid,zero,overflow" COPTIMIZE="-g     -ffpe-trap=invalid,zero,overflow" nwchem_config

32 #make DIAG=PAR FC=gfortran CC=gcc CDEBUG="-g -ffpe-trap=invalid,zero,overflow" FDEBUG="-g -ffpe-trap=invalid,zero,overflow" FOPTIMIZE="-g -ffpe-trap=invalid,zero,overflow" COPTIMIZE="-g     -ffpe-trap=invalid,zero,overflow" $1

33 #make DIAG=PAR FC=gfortran CC=gcc CDEBUG="-pg -g" FDEBUG="-pg -g" FOPTIMIZE="-pg -g -O0" COPTIMIZE="-pg -g -O0" nwchem_config

34 #make DIAG=PAR FC=gfortran CC=gcc CDEBUG="-pg -g" FDEBUG="-pg -g" FOPTIMIZE="-pg -g -O0" COPTIMIZE="-pg -g -O0" $1

35 make realclean

36

37 make FC=gfortran _GCC4=Y CC=gcc nwchem_config

38 #make DIAG=PAR FC=gfortran CC=gcc nwchem_config

39 make DIAG=PAR FC=gfortran CC=gcc $1

Forum Vet

10:09:59 AM PDT - Mon, Sep 28th 2015
Nope, I am asking you what is the output of cd $NWCHEM_TOP/src make link PS Please do not redefine FOPTIMIZE and COPTIMIZE since it's a recipe for impending disaster

Clicked A Few Times

11:41:31 PM PDT - Mon, Sep 28th 2015
Ok, sorry. Here is the output: make nwchem.o stubs.o make[1]: warning: -jN forced in submake: disabling jobserver mode. Converting nwchem.F -> nwchem.f Converting stubs.F -> stubs.f f77 -c -g -g stubs.f /bin/sh: f77: command not found make[1]: * [stubs.o] Error 127 make[1]: * Waiting for unfinished jobs.... f77 -c -g -g nwchem.f /bin/sh: f77: command not found make[1]: * [nwchem.o] Error 127 make: * [link] Error 2

Forum Vet

9:50:08 AM PDT - Tue, Sep 29th 2015
I am asking you what is the output of cd $NWCHEM_TOP/src make FC=gfortran LIBMPI=" -lmpichf90 -lmpichf90 -lmpich" MPI_LIB=/usr/local/parastation/mpi2-intel12-mt-5.0.27-1/lib link

Clicked A Few Times

2:15:04 AM PDT - Mon, Oct 5th 2015

It is a little bit long, but I attach it below

ntel12-mt-5.0.27-1/lib link
make nwchem.o stubs.o
make[1]: warning: -jN forced in submake: disabling jobserver mode.
Converting nwchem.F -> nwchem.f
Converting stubs.F -> stubs.f
gfortran -c -g -g stubs.f
stubs.f:1.1:

/* Copyright (C) 1991-2012 Free Software Foundation, Inc.

Error: Non-numeric character in statement label at (1)
stubs.f:1.2:

/* Copyright (C) 1991-2012 Free Software Foundation, Inc.

Error: Invalid character in name at (1)
stubs.f:2.4:

  This file is part of the GNU C Library.

   1

Error: Non-numeric character in statement label at (1)
stubs.f:2.4:

  This file is part of the GNU C Library.

   1

Error: Unclassifiable statement at (1)
stubs.f:4.4:

  The GNU C Library is free software; you can redistribute it and/or

   1

Error: Non-numeric character in statement label at (1)
stubs.f:4.4:

  The GNU C Library is free software; you can redistribute it and/or

   1

Error: Unclassifiable statement at (1)
stubs.f:4.38:

  The GNU C Library is free software; you can redistribute it and/or

                                     1

Error: Unclassifiable statement at (1)
stubs.f:5.4:

  modify it under the terms of the GNU Lesser General Public

   1

Error: Non-numeric character in statement label at (1)
stubs.f:5.4:

  modify it under the terms of the GNU Lesser General Public

   1

Error: Unclassifiable statement at (1)
stubs.f:6.4:

  License as published by the Free Software Foundation; either

   1

Error: Non-numeric character in statement label at (1)
stubs.f:6.4:

  License as published by the Free Software Foundation; either

   1

Error: Unclassifiable statement at (1)
stubs.f:6.56:

  License as published by the Free Software Foundation; either

                                                       1

Error: Unclassifiable statement at (1)
stubs.f:7.4:

  version 2.1 of the License, or (at your option) any later version.

   1

Error: Non-numeric character in statement label at (1)
stubs.f:7.4:

  version 2.1 of the License, or (at your option) any later version.

   1

Error: Unclassifiable statement at (1)
stubs.f:9.4:

  The GNU C Library is distributed in the hope that it will be useful,

   1

Error: Non-numeric character in statement label at (1)
stubs.f:9.4:

  The GNU C Library is distributed in the hope that it will be useful,

   1

Error: Unclassifiable statement at (1)
stubs.f:10.4:

  but WITHOUT ANY WARRANTY; without even the implied warranty of

   1

Error: Non-numeric character in statement label at (1)
stubs.f:10.4:

  but WITHOUT ANY WARRANTY; without even the implied warranty of

   1

Error: Unclassifiable statement at (1)
stubs.f:10.28:

  but WITHOUT ANY WARRANTY; without even the implied warranty of

                           1

Error: Unclassifiable statement at (1)
stubs.f:11.4:

  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU

   1

Error: Non-numeric character in statement label at (1)
stubs.f:11.4:

  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU

   1

Error: Unclassifiable statement at (1)
stubs.f:12.4:

  Lesser General Public License for more details.

   1

Error: Non-numeric character in statement label at (1)
stubs.f:12.4:

  Lesser General Public License for more details.

   1

Error: Unclassifiable statement at (1)
stubs.f:14.4:

  You should have received a copy of the GNU Lesser General Public

   1

Error: Non-numeric character in statement label at (1)
stubs.f:14.4:

  You should have received a copy of the GNU Lesser General Public

   1

Error: Unclassifiable statement at (1)
Fatal Error: Error count reached limit of 25.
make[1]: *** [stubs.o] Error 1
make[1]: *** Waiting for unfinished jobs....
gfortran -c -g -g nwchem.f
nwchem.f:1.1:

/* Copyright (C) 1991-2012 Free Software Foundation, Inc.

Error: Non-numeric character in statement label at (1)
nwchem.f:1.2:

/* Copyright (C) 1991-2012 Free Software Foundation, Inc.

Error: Invalid character in name at (1)
nwchem.f:2.4:

  This file is part of the GNU C Library.

   1

Error: Non-numeric character in statement label at (1)
nwchem.f:2.4:

  This file is part of the GNU C Library.

   1

Error: Unclassifiable statement at (1)
nwchem.f:4.4:

  The GNU C Library is free software; you can redistribute it and/or

   1

Error: Non-numeric character in statement label at (1)
nwchem.f:4.4:

  The GNU C Library is free software; you can redistribute it and/or

   1

Error: Unclassifiable statement at (1)
nwchem.f:4.38:

  The GNU C Library is free software; you can redistribute it and/or

                                     1

Error: Unclassifiable statement at (1)
nwchem.f:5.4:

  modify it under the terms of the GNU Lesser General Public

   1

Error: Non-numeric character in statement label at (1)
nwchem.f:5.4:

  modify it under the terms of the GNU Lesser General Public

   1

Error: Unclassifiable statement at (1)
nwchem.f:6.4:

  License as published by the Free Software Foundation; either

   1

Error: Non-numeric character in statement label at (1)
nwchem.f:6.4:

  License as published by the Free Software Foundation; either

   1

Error: Unclassifiable statement at (1)
nwchem.f:6.56:

  License as published by the Free Software Foundation; either

                                                       1

Error: Unclassifiable statement at (1)
nwchem.f:7.4:

  version 2.1 of the License, or (at your option) any later version.

   1

Error: Non-numeric character in statement label at (1)
nwchem.f:7.4:

  version 2.1 of the License, or (at your option) any later version.

   1

Error: Unclassifiable statement at (1)
nwchem.f:9.4:

  The GNU C Library is distributed in the hope that it will be useful,

   1

Error: Non-numeric character in statement label at (1)
nwchem.f:9.4:

  The GNU C Library is distributed in the hope that it will be useful,

   1

Error: Unclassifiable statement at (1)
nwchem.f:10.4:

  but WITHOUT ANY WARRANTY; without even the implied warranty of

   1

Error: Non-numeric character in statement label at (1)
nwchem.f:10.4:

  but WITHOUT ANY WARRANTY; without even the implied warranty of

   1

Error: Unclassifiable statement at (1)
nwchem.f:10.28:

  but WITHOUT ANY WARRANTY; without even the implied warranty of

                           1

Error: Unclassifiable statement at (1)
nwchem.f:11.4:

  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU

   1

Error: Non-numeric character in statement label at (1)
nwchem.f:11.4:

  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU

   1

Error: Unclassifiable statement at (1)
nwchem.f:12.4:

  Lesser General Public License for more details.

   1

Error: Non-numeric character in statement label at (1)
nwchem.f:12.4:

  Lesser General Public License for more details.

   1

Error: Unclassifiable statement at (1)
nwchem.f:14.4:

  You should have received a copy of the GNU Lesser General Public

   1

Error: Non-numeric character in statement label at (1)
nwchem.f:14.4:

  You should have received a copy of the GNU Lesser General Public

   1

Error: Unclassifiable statement at (1)
Fatal Error: Error count reached limit of 25.
make[1]: *** [nwchem.o] Error 1
make: *** [link] Error 2

Forum Vet

10:05:58 AM PDT - Mon, Oct 5th 2015
Could you please try the 6.6 beta version since the MPI part of the installation has been simplified? Please unset all the MPI env. variables (MPI_LIB LIBMPI and MPI_INCLUDE). You simply need mpif90 to be in your path Download instructions at http://nwchemgit.github.io/index.php/Download#Download_the_beta_version_of_the_NWChem_6.6_Re...

Clicked A Few Times

8:25:31 AM PST - Sun, Nov 29th 2015

Dear Edoapra,
thank you for your precious advice. Unfrotunately, I still have some problems to run in parallel which I think are due to the compilation step. I attach my current makefile:

 1 #!/bin/bash

 3 module load intel

 4 export USE_SUBGROUPS=y

 5 export USE_MPI=y

 6 export USE_MPIF=y

 7 export USE_MPIF4=y

 9 export MSG_COMMS=MPI

10 export USE_PYTHON64=yes

11 export MPI_LOC=/usr/local/software/jureca/Stage3/software/Toolchain/iccifort/2015.3.187-GCC-bare-4.9.3/impi/5.1.0.079/intel64/

12 export USE_SCALAPACK=y

13 export SCALAPACK "location of Scalapack and BLACS library"

14 export USE_INTERNALBLAS=y

21 export ARMCI_NETWORK=OPENIB

22 export PYTHONHOME=/usr/bin

23 export PYTHONVERSION=2.6

24 export NWCHEM_TOP=`pwd`

25 export NWCHEM_TARGET=LINUX64

27 export NWCHEM_MODULES="all"

28 export NWCHEM_EXECUTABLE=$NWCHEM_TOP/bin/LINUX64/nwchem

29 export PYTHONPATH=./:$NWCHEM_TOP/contrib/python/

30 export LARGE_FILES=TRUE

31 export ENABLE_COMPONENT=yes

32 export TCGGRSH=/usr/bin/ssh

33 export FOPTIMIZE="-O3 -xSSE2,SSE3,SSSE3,SSE4.1,SSE4.2 -no-prec-div -funroll-loops -unroll-aggressive"

34 export COPTIMIZE="-O3 -xSSE2,SSE3,SSSE3,SSE4.1,SSE4.2 -no-prec-div -funroll-loops"

35 cd $NWCHEM_TOP/src

40 make realclean

41

42 make FC=gfortran _GCC4=Y CC=gcc nwchem_config

44 make DIAG=PAR FC=gfortran CC=gcc $1

When trying to run a job, a single task is exectude. For the other tasks I get the following error:

Last System Error Message from Task 696:: No such file or directory

I am using a machine in which software is organized through a hierarchy of modules. So I loaded Intel module (which contains icc/ifort + Intel MPI) at the beginning of the script.
Any ideas about the origin of this problem?

Thank you
Alessandro

Forum >> NWChem's corner >> Compiling NWChem