Fail to run 2 example jobs

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Dear all,

I got a copy of NWChem 6.0 and compiled on a linux cluster with infiniband connection (OPENIB) using different combinations of compiler and mpi: includes gcc/gfortran, gcc/ifort with intel mpi and openMPI.

I run 2 example jobs in a linux cluster using 4 processor on 4 nodes, and they are fail as described in the following:

(1) "SiC 8 atom cubic cell - geometry and unit cell optimization"; the job fail with the following message


(rank:3 hostname:fuji450 pid:19313):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0
 geom_cart_coords_get: open geometies:  1
  1 geom_cart_coords_get: "geometry" -> "geometry"
 geom_cart_coords_get: geometries in last accessed data base:  2
 geometry
 driverinitial
 _______________________________________________________
 load_cellgeometry: geom cart?        0
 _______________________________________________________
 _______________________________________________________
  current input line :
    40: task paw optimize
 _______________________________________________________
 _______________________________________________________
 There is an error related to the specified geometry
 _______________________________________________________

Here is the input of SiC example
SiC 8 atom cubic cell - geometry and unit cell optimization


(2) "Diamond 8 atom cubic cell - geometry and unit cell optimization", and I got another error :
          |S|      = 0.14343E-02
          pressure = 0.828E-03 au
                   = 0.244E+00 Mbar
                   = 0.244E+02 GPa
                   = 0.240E+06 atm


 Writing Crystallographic Information File:./perm/diamond111.opt.cif
   - cell not shifted (nwpw:cif_shift_cell .false.)
At line 2482 of file ion.F (unit = 19, file = './perm/diamond111.opt.cif')
Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE


and here is the input
Diamond 8 atom cubic cell - geometry and unit cell optimization

Can anyone tell me what was the problem and provide me a fix? Thanks a lot.

Regards
Dominic Chien
Edited On 12:52:55 AM PDT - Mon, Aug 15th 2011 by Chiensh

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Can you please send me your outputs. I just ran these examples with 4cpus w/o any problem

Eric Bylaska

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The Fortran runtime error is possibly a GCC version problem?
Hi - I have received a similar error (though in a different place) after building nwchem6 with GCC 4.6.1:

"At line 623 of file psp_generator_input.F (unit = 99, file = '/tmp/gelb/pysim/single-config/junk.inp')
Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE"

When I rebuilt with GCC 4.4.6, this error disappeared. There was a change in the compiler that had something to do with this (GCC Bug 44477), but I'm not sure what.

(Also - in doing this I discovered that if your 'gfortran' compiler is named, say, 'gfortran-4.6', then the stuff in config/makefile.h doesn't see it and all the compilation flags get set incorrectly.)

Cheers,

Lev Gelb

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I got today the same error for psp_generator_input.F ("Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE", etc) and I used gcc 4.7.2 under LInux Mint to compile nwchem 6.1.1.

Does anybody know which gcc version should I use ? The Software manager has gcc 4.4, 4.5, 4.6 and 4.7.

Thank you very much,
Mickey

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MIckey
Could you please post the complete error message you got.
What is the compilation command you have used?
Could you please post the env. variable settings used, too?
Thanks, Edo
Quote:MickeyM Apr 14th 5:59 pm
I got today the same error for psp_generator_input.F ("Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE", etc) and I used gcc 4.7.2 under LInux Mint to compile nwchem 6.1.1.

Does anybody know which gcc version should I use ? The Software manager has gcc 4.4, 4.5, 4.6 and 4.7.

Thank you very much,
Mickey

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Quote:Edoapra Apr 15th 11:31 am
MIckey
Could you please post the complete error message you got.
What is the compilation command you have used?
Could you please post the env. variable settings used, too?
Thanks, Edo


Dear Edo,
The mesage was :


library name resolved from: compiled reference
NWCHEM_NWPW_LIBRARY set to: </home/michi/Downloads/nwchem-6.1.1-src/src/nwpw/libraryps/>
Generating 1d pseudopotential for C
At line 649 of file psp_generator_input.F (unit = 99, file = './scratch/junk.inp')
Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE




and my installation followed nwchem standard rules:


export NWCHEM_TOP=/home/michi/Downloads/nwchem-6.1.1-src
export NWCHEM_TARGET=LINUX
export FC=gfortran
export CC=gcc
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export LIBMPI="-lmpich -lopa -lmpl -lrt -lpthread"
export MPI_LIB=/usr/lib/mpich2/lib
export MPI_INCLUDE=/usr/lib/mpich2/include
export NWCHEM_MODULES=all
export LARGE_FILES=TRUE
export USE_NOFSCHECK=TRUE
export LIB_DEFINES=-DDFLT_TOT_MEM=16777216

cd $NWCHEM_TOP/src
make nwchem_config
make >& make.log


Best regards,
Mickey

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gfortran version
Mickey
Thank you very much for the feedback you have provided.
I need some information about the gfortran version you are using. What is the output you get from the following command?
gfortran -dumpversion

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LINUX vs LINUX64
Mickey
Is there any particular reason why you are using LINUX as NWCHEM_TARGET instead of the 64-bit option LINUX64?
What is the output of the command "uname -a" on your system?

Thanks, Edo
Edited On 5:16:10 PM PDT - Fri, Apr 19th 2013 by Edoapra

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Both gfortran and gcc are 4.7
I am using LINUX becasue I have a 32 bit Linux Mint 14.
The output of uname -a is
Linux PHYS142331 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 i686 i686 i686 GNU/Linux
Best regards,
Mickey

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Mickey,
Please apply the patch provided below to makefile.h and recompile the nwpw directory
http://www.nwchem-sw.org/images/Gcc46_nw611.patch.gz

This are the steps you need to take
1) cd $NWCHEM_TOP/src/config
2) wget http://www.nwchem-sw.org/images/Gcc46_nw611.patch.gz
3) gzip -d Gcc46_nw611.patch.g
4) patch -p0 < Gcc46_nw611.patch
5) cd ../nwpw
6) make FC=gfortran clean
7) make FC=gfortran
8) cd ..
9) make FC=gfortran link

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I try diamond-band.nw from 1st post with NWChem source code February 06, 2013 but have the similar error

At line 649 of file psp_generator_input.F (unit = 99, file = './scratch/junk.inp')
Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE

I thought that this error was fixed.

gcc -v
Using built-in specs.
COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.7.2/gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/4.7.2/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /mnt/slag/portage/sys-devel/gcc-4.7.2-r1/work/gcc-4.7.2/configure --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.7.2 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.7.2 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.7.2/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.7.2/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/include/g++-v4 --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --disable-altivec --disable-fixed-point --with-ppl --with-cloog --disable-ppl-version-check --with-cloog-include=/usr/include/cloog-ppl --enable-lto --enable-nls --without-included-gettext --with-system-zlib --enable-obsolete --disable-werror --enable-secureplt --enable-multilib --with-multilib-list=m32,m64 --enable-libmudflap --disable-libssp --enable-libgomp --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.7.2/python --enable-checking=release --enable-java-awt=gtk --enable-libstdcxx-time --enable-objc-gc --enable-languages=c,c++,java,go,objc,obj-c++,fortran --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-targets=all --with-bugurl=http://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.7.2-r1 p1.5, pie-0.5.5'
Thread model: posix
gcc version 4.7.2 (Gentoo 4.7.2-r1 p1.5, pie-0.5.5)


gfortran -v
Using built-in specs.
COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.7.2/gfortran
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/4.7.2/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /mnt/slag/portage/sys-devel/gcc-4.7.2-r1/work/gcc-4.7.2/configure --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.7.2 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.7.2 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.7.2/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.7.2/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/include/g++-v4 --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --disable-altivec --disable-fixed-point --with-ppl --with-cloog --disable-ppl-version-check --with-cloog-include=/usr/include/cloog-ppl --enable-lto --enable-nls --without-included-gettext --with-system-zlib --enable-obsolete --disable-werror --enable-secureplt --enable-multilib --with-multilib-list=m32,m64 --enable-libmudflap --disable-libssp --enable-libgomp --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.7.2/python --enable-checking=release --enable-java-awt=gtk --enable-libstdcxx-time --enable-objc-gc --enable-languages=c,c++,java,go,objc,obj-c++,fortran --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-targets=all --with-bugurl=http://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.7.2-r1 p1.5, pie-0.5.5'
Thread model: posix
gcc version 4.7.2 (Gentoo 4.7.2-r1 p1.5, pie-0.5.5)

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Viktor,
Could you please recompile
$NWCHEM_TOP/src/nwpw/nwpwlib/pseudopotential/
and post the output of your compilation command?

Could you send the output of the following command, too
gfortran -dumpversion

Thanks,. Edo

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Viktor
I have just tried the Feb 06 binary under Gentoo with gcc 4.7.2 and the diamond test ran to completion.

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gfortran -dumpversion
4.7.2


For compilation NWChem I use ebuild from https://bugs.gentoo.org/show_bug.cgi?id=393139 after modification for Nwchem-src-2013-02-06.

Maybe something is wrong at these ebuild.


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