The issue:
If, on debian testing/wheezy 64 bit with gcc 4.7, you run the following using NWChem 6.1.1
You'll end up withTitle "boric acid" Start boric echo charge 0 geometry autosym units angstrom B 0.00000 0.00000 0.00000 O -4.93432e-17 1.55000 0.00000 H 1.06537 1.92667 0.00000 O 1.34234 -0.775000 0.00000 H 1.13586 -1.88597 0.00000 O -1.34234 -0.775000 0.00000 H -2.20123 -0.0406974 0.00000 end ecce_print ecce.out nwpw mult 1 xc pbe96 cutoff 90.0 np_dimensions -1 -1 tolerances 1e-7 1e-7 car-parrinello nose-hoover 1.000000e+03 2.981500e+02 1.000000e+03 2.981500e+02 time_step 0.500000e+00 fake_mass 1.000000e+02 loop 10 100 scaling 1.000000e+00 1.000000e+00 end end task pspw energy task pspw car-parrinello
**************************************************** * * * NWPW PSPW Calculation * * * * [ (Grassman/Stiefel manifold implementation) ] * * * * [ NorthWest Chemistry implementation ] * * * * version #5.10 06/12/02 * * * * This code was developed by Eric J. Bylaska, * * and was based upon algorithms and code * * developed by the group of Prof. John H. Weare * * * **************************************************** >>> JOB STARTED AT Mon Apr 15 10:05:42 2013 <<< ================ input data ======================== library name resolved from: compiled reference NWCHEM_NWPW_LIBRARY set to: Generating 1d pseudopotential for B At line 649 of file psp_generator_input.F (unit = 99, file = './junk.inp') Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE -------------------------------------------------------------------------- mpirun has exited due to process rank 0 with PID 28100 on node neon exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------
The fix
/opt/nwchem/nwchem-6.1.1-src is the NWCHEM_TOP of my particular nwchem source. See e.g. here for build instructions in general and not that e.g. BLASOPT settings etc. correspond to what I need on my system. Modify as necessary.
cd /opt/nwchem/nwchem-6.1.1-src/ wget http://www.nwchem-sw.org/images/Makefile.h.gcc46.patch.gz gunzip Makefile.h.gcc46.patch.gz patch -p0 < Makefile.h.gcc46.patch cd src/nwpw/ touch `egrep -l GCC46 */*/*F` export LARGE_FILES=TRUE export TCGRSH=/usr/bin/ssh export NWCHEM_TOP=/opt/nwchem/nwchem-6.1.1-src export NWCHEM_TARGET=LINUX64 export NWCHEM_MODULES="all" export PYTHONHOME=/usr export BLASOPT="-L/opt/acml/acml5.2.0/gfortran64_fma4_int64/lib -lacml" export USE_MPI=y export USE_MPIF=y export USE_MPIF4=y export MPI_LOC=/usr/lib/openmpi/lib export MPI_INCLUDE=/usr/lib/openmpi/include export LIBRARY_PATH="$LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/acml/acml5.2.0/gfortran64_fma4_int64/lib" export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread" export FC=gfortran make cd ../ make link ./getmem.nwchem
Because we just relink instead of recompiling from scratch, recompiling is fairly quick (2-3 minutes in total)
Testing
It now continues as it should:
================ input data ======================== library name resolved from: compiled reference NWCHEM_NWPW_LIBRARY set to: Generating 1d pseudopotential for B
and everything is good from there-on.
NOTE: you need to delete the output files from any previous run, or you might end up with errors during the Car-Parrinello portion (e.g.
At line 170 of file MOTION.F (unit = 19, file = './boric.ion_motion'))
Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE
Stay tuned...
What remains for me is to start collecting the patches that are needed for nwchem to work properly (from my perspective -- I only have to support myself and my debian boxes, not a heterogeneous set of users with equally heterogeneous hardware, so my job is easier than that of the nwchem devs) so that installing and upgrading nwchem becomes less painful (yes, I've been patching by hand up till now...).
The issues that need to be patched are:
* including libz and libssl on debian when building with python support (e.g. step 1 in this post)
* changing the details in the output to support gabEdit (e.g. this post)
* patching for GCC 4.7 (i.e. what you've just read)
Update: The post is here now: http://verahill.blogspot.com.au/2013/04/389-patches-for-nwchem-611-on-debian.html
