From NWChem
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Posts 13
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| 3:00:37 AM PST - Wed, Jan 11th 2017 |
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Hi everyone,
I keep receiving this error over and over again:
...
NWChem Input Module
-------------------
WATER 6-311G* meta-GGA XC geometry
----------------------------------
Scaling coordinates for geometry "geometry" by 1.889725989
(inverse scale = 0.529177249)
C2V symmetry detected
------
auto-z
------
------------------------------------------------------------------------
geom_binvr: dsyev failed 25769803776
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
10: end
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
For more information see the NWChem manual at http://www.nwchem-sw.org/index.php/NWChem_Documentation
For further details see manual section:
0:geom_binvr: dsyev failed:Received an Error in Communication
MPI: Global rank 0 is aborting with error code 0.
Process ID: 31348, Host: r1i0n11, Program: /opt/local/nwchem-6.6/bin/nwchem
...
Then MPI starts complaining:
...
MPI: --------stack traceback-------
MPI: Attaching to program: /proc/31348/exe, process 31348
MPI: Try: zypper install -C "debuginfo(build-id)=06659f9e2a7c2cbd7771266eca5d573397f3ade3"
MPI: (no debugging symbols found)...done.
MPI: Try: zypper install -C "debuginfo(build-id)=4e9fa1a2c1141fc0123a142783efd044c40bdaaf"
MPI: (no debugging symbols found)...done.
MPI: Try: zypper install -C "debuginfo(build-id)=3f06bcfc74f9b01780d68e89b8dce403bef9b2e3"
MPI: (no debugging symbols found)...done.
MPI: Try: zypper install -C "debuginfo(build-id)=f7b8fc2bc1d68899a2cb561ac8e16092228223e3"
MPI: (no debugging symbols found)...done.
MPI: Try: zypper install -C "debuginfo(build-id)=f607b21f9a513c99bba9539050c01236d19bf22b"
MPI: (no debugging symbols found)...done.
MPI: Try: zypper install -C "debuginfo(build-id)=d44cbcbbcbdc9ed66abdcd82fa04fb4140bc155e"
MPI: (no debugging symbols found)...done.
MPI: Try: zypper install -C "debuginfo(build-id)=c1807b5762068e6c5f4a6a0ed48d9d4469965351"
MPI: (no debugging symbols found)...done.
MPI: Try: zypper install -C "debuginfo(build-id)=f69d3b06516c61cfab7d00c9ef86c41936dfc017"
MPI: (no debugging symbols found)...done.
MPI: [Thread debugging using libthread_db enabled]
MPI: Try: zypper install -C "debuginfo(build-id)=7bcdd7deb661fbb367edf63273568fc962aefbed"
MPI: (no debugging symbols found)...done.
MPI: Try: zypper install -C "debuginfo(build-id)=7d7940c46e5ea77fb4896ce5dba45bc9299c5e0c"
MPI: (no debugging symbols found)...done.
MPI: Try: zypper install -C "debuginfo(build-id)=02c78a8ec7997130f18f6c4fdef78ed36b853133"
MPI: (no debugging symbols found)...done.
MPI: Try: zypper install -C "debuginfo(build-id)=f1e396fe2fd218a097a0fe16bd3e8951056cb0e6"
MPI: (no debugging symbols found)...done.
MPI: 0x00002af1c9762b15 in waitpid () from /lib64/libc.so.6
MPI: (gdb) #0 0x00002af1c9762b15 in waitpid () from /lib64/libc.so.6
MPI: #1 0x00002af1c8cf5074 in mpi_sgi_system (command=<optimized out>) at sig.c:88
MPI: #2 MPI_SGI_stacktraceback (header=<optimized out>) at sig.c:271
MPI: #3 0x00002af1c8c88062 in print_traceback (ecode=0) at abort.c:168
MPI: #4 0x00002af1c8c8830b in PMPI_Abort (comm=<optimized out>, errorcode=0) at abort.c:59
MPI: #5 0x0000000002bd8957 in wnga_error ()
MPI: #6 0x0000000002b8bf21 in ga_error_ ()
MPI: #7 0x0000000000a27a94 in errquit (string=@0x2ec9410, icode=@0x7fff972d96d0, errcode=@0x2ec9408, _string=24) at errquit.F:144
MPI: #8 0x0000000000a04782 in geom_binvr_ ()
MPI: #9 0x0000000000a05a49 in geom_bandbi_ ()
MPI: #10 0x00000000009cb9f2 in geom_impose_constraints (geom=@0x7fff972f1728, impose_constraints=0x9cb375 <geom_impose_initial_values_on_q>) at geom_i
nput.F:7147
MPI: #11 0x00000000009e9814 in geom_input (rtdb=@0x7fff972f1e38) at geom_input.F:690
MPI: #12 0x0000000000408a81 in input_parse (rtdb=@0x7fff972f1e38) at input_parse.F:64
MPI: #13 0x00000000004075fe in nwchem () at nwchem.F:275
MPI: #14 0x0000000002cc076c in main (argc=2, argv=0x7fff972f1f98) at ../../../libgfortran/fmain.c:21
MPI: #15 0x00002af1c96debc6 in __libc_start_main () from /lib64/libc.so.6
MPI: #16 0x0000000000405d59 in _start () at ../sysdeps/x86_64/elf/start.S:113
MPI: (gdb) A debugging session is active.
MPI:
MPI: Inferior 1 [process 31348] will be detached.
MPI:
MPI: Quit anyway? (y or n) [answered Y; input not from terminal]
MPI: Detaching from program: /proc/31348/exe, process 31348
MPI: -----stack traceback ends-----
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job
Here is my input file:
# taken directly from
# <http://www.nwchem-sw.org/index.php/Release66:Density_Functional_Theory_for_Molecules#Sample_input_file>
title "WATER 6-311G* meta-GGA XC geometry"
echo
geometry units angstroms
O 0.0 0.0 0.0
H 0.0 0.0 1.0
H 0.0 1.0 0.0
end
basis
H library 6-311G*
O library 6-311G*
end
dft
iterations 50
print kinetic_energy
xc xtpss03 ctpss03
decomp
end
task dft optimize
task dft freq numerical
and, as the comment says, it was taken directly from the documentation, so it's supposed to run OK.
I suspect it has to do with either parallelization (we're using MPT 2.03) or compiling.
Any clues? Thanks in advance.
All the best,
Felipe
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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Forum Vet
Threads 8
Posts 1371
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| 5:18:38 PM PST - Mon, Jan 16th 2017 |
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Please post the output of the following commands
env | grep BLAS
env | grep USE
ldd $NWCHEM_TOP/bin/LINUX64/nwchem
head -24 $NWCHEM_TOP/src/tools/build/config.log
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Edited On 5:19:13 PM PST - Mon, Jan 16th 2017 by Edoapra
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Clicked A Few Times
Threads 4
Posts 13
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| 9:08:10 AM PST - Tue, Jan 17th 2017 |
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Hi,
Quote:Edoapra Jan 17th 1:18 amPlease post the output of the following commands
env | grep BLAS
env | grep USE
ldd $NWCHEM_TOP/bin/LINUX64/nwchem
head -24 $NWCHEM_TOP/src/tools/build/config.log
The first gives me nothing, the second gives:
$ env | grep USE
USER=dudektri
which is only my user name.
The complete env is as follows:
$ env
MPI_BUFS_PER_PROC=256
MODULE_VERSION_STACK=3.1.6
MKLROOT=/opt/intel/composerxe-2011.0.084/mkl
LESSKEY=/etc/lesskey.bin
LC_PAPER=pt_BR.UTF-8
NNTPSERVER=news
INFODIR=/usr/local/info:/usr/share/info:/usr/info
MANPATH=/opt/mpi/sgi/man:/opt/local/share/man:/opt/local/gromacs/share/man:/opt/intel/composerxe-2011.0.084/man/en_US:/opt/intel/composerxe-2011.0.084/man/en_US:/usr/local/man:/usr/local/share/man:/usr/share/man:/usr/man:/opt/c3/man:/usr/share/catman:/usr/catman:/opt/pbs/default/man:/opt/sgi/share/man
LC_ADDRESS=pt_BR.UTF-8
HOSTNAME=gauss
LC_MONETARY=pt_BR.UTF-8
XKEYSYMDB=/usr/share/X11/XKeysymDB
_MODULESBEGINENV_=/home/u/dudektri/.modulesbeginenv
INTEL_LICENSE_FILE=/opt/intel/composerxe-2011.0.084/licenses:/opt/intel/licenses:/home/u/dudektri/intel/licenses
HOST=gauss
TERM=xterm-256color
SHELL=/bin/bash
PROFILEREAD=true
HISTSIZE=1000
SSH_CLIENT=150.162.31.44 40556 22
LIBRARY_PATH=/opt/mpi/sgi/lib:/opt/intel/composerxe-2011.0.084/compiler/lib/intel64:/opt/intel/composerxe-2011.0.084/compiler/lib/intel64:/opt/intel/composerxe-2011.0.084/mkl/lib/intel64
FPATH=/opt/mpi/sgi/include:/opt/intel/composerxe-2011.0.084/mkl/include
MORE=-sl
LC_NUMERIC=pt_BR.UTF-8
QTDIR=/usr/lib/qt3
GMXMAN=/opt/local/gromacs/share/man
OLDPWD=/home/u/dudektri
MIC_LD_LIBRARY_PATH=/opt/intel/composerxe-2011.0.084/compiler/lib/mic
SSH_TTY=/dev/pts/9
JRE_HOME=/usr/lib64/jvm/jre
USER=dudektri
LS_COLORS=rs=0:di=01;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:
MPI_BUFFER_MAX=2048
LD_LIBRARY_PATH=/opt/local/R/lib:/opt/local/python/lib:/opt/local/gnu/netcdf/lib:/opt/local/gnu/hdf5/lib:/opt/mpi/sgi/lib:/opt/local/lib:/opt/local/gromacs/lib:/opt/local/gnu/fftw/lib:/opt/intel/composerxe-2011.0.084/compiler/lib/intel64:/opt/intel/composerxe-2011.0.084/mpirt/lib/intel64:/opt/intel/composerxe-2011.0.084/compiler/lib/intel64:/opt/intel/composerxe-2011.0.084/mkl/lib/intel64
LC_TELEPHONE=pt_BR.UTF-8
XNLSPATH=/usr/share/X11/nls
ENV=/etc/bash.bashrc
OSCAR_HOME=/opt/oscar
CPATH=/opt/mpi/sgi/include:/opt/intel/composerxe-2011.0.084/mkl/include
HOSTTYPE=x86_64
FROM_HEADER=
GMXDATA=/opt/local/gromacs/share/gromacs
PAGER=less
CSHEDIT=emacs
ANYRC=true
XDG_CONFIG_DIRS=/etc/xdg
NLSPATH=/opt/intel/composerxe-2011.0.084/compiler/lib/intel64/locale/%l_%t/%N:/opt/intel/composerxe-2011.0.084/mkl/lib/intel64/locale/%l_%t/%N:/opt/intel/composerxe-2011.0.084/debugger/intel64/locale/%l_%t/%N
MINICOM=-c on
MODULE_VERSION=3.1.6
MAIL=/var/mail/dudektri
PATH=/home/u/dudektri/.bin:/home/u/dudektri/bin:/opt/local/R/bin:/opt/local/python/bin:/opt/local/gnu/netcdf/bin:/opt/local/gnu/hdf5/bin:/opt/mpi/sgi/bin:/opt/local/bin:/opt/local/gromacs/bin:/opt/intel/composerxe-2011.0.084/bin/intel64:/opt/intel/composerxe-2011.0.084/mpirt/bin/intel64:/opt/local/cmake/bin:/home/u/dudektri/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib64/jvm/jre/bin:/opt/c3/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/local/maple15/bin:/opt/local/MATLAB/R2014a/bin:/opt/pbs/default/bin:.:/usr/lib/qt3/bin:/opt/sgi/sbin:/opt/sgi/bin:/opt/local/gnu/wrf
CPU=x86_64
JAVA_BINDIR=/usr/lib64/jvm/jre/bin
SSH_SENDS_LOCALE=yes
LC_IDENTIFICATION=pt_BR.UTF-8
R_LIBS=/home/u/dudektri/.rlibs
MPI_IB_PAYLOAD=128
MLM_LICENSE_FILE=27010@gauss
DADOS=/dados/dudektri
INPUTRC=/etc/inputrc
PWD=/home/u/dudektri
_LMFILES_=/opt/local/share/modules/modulefiles/mpt/2.03
JAVA_HOME=/usr/lib64/jvm/jre
EDITOR=vim
LANG=en_US.UTF-8
PYTHONSTARTUP=/etc/pythonstart
MODULEPATH=/opt/local/share/modules/modulefiles:/usr/share/modules:/usr/share/modules/modulefiles
LOADEDMODULES=mpt/2.03
LC_MEASUREMENT=pt_BR.UTF-8
C3_RSH=ssh -oConnectTimeout=10 -oForwardX11=no
QT_SYSTEM_DIR=/usr/share/desktop-data
SHLVL=1
HOME=/home/u/dudektri
LESS_ADVANCED_PREPROCESSOR=no
OSTYPE=linux
LS_OPTIONS=-N --color=tty -T 0
XCURSOR_THEME=crystalwhite
WINDOWMANAGER=/usr/bin/gnome
MPI_BUFS_THRESHOLD=1
GNUTERM=dumb
G_FILENAME_ENCODING=@locale,UTF-8,ISO-8859-15,CP1252
MPI_ROOT=/opt/mpi/sgi
GMXBIN=/opt/local/gromacs/bin
LESS=-M -I
MACHTYPE=x86_64-suse-linux
LOGNAME=dudektri
CVS_RSH=ssh
XDG_DATA_DIRS=/usr/share:/etc/opt/kde3/share:/opt/kde3/share
GMXLDLIB=/opt/local/gromacs/lib
SSH_CONNECTION=150.162.31.44 40556 143.54.22.90 22
LC_CTYPE=pt_BR.UTF-8
MODULESHOME=/usr/share/modules
PKG_CONFIG_PATH=/opt/local/gromacs/lib/pkgconfig
LESSOPEN=lessopen.sh %s
INFOPATH=/usr/local/info:/usr/share/info:/usr/info
INCLUDE=/opt/local/python/include:/opt/intel/composerxe-2011.0.084/mkl/include
LESSCLOSE=lessclose.sh %s %s
LC_TIME=pt_BR.UTF-8
G_BROKEN_FILENAMES=1
JAVA_ROOT=/usr/lib64/jvm/jre
COLORTERM=1
LC_NAME=pt_BR.UTF-8
_=/usr/bin/env
The third (path adapted to suit the cluster):
$ ldd /opt/local/nwchem/bin/nwchem
linux-vdso.so.1 => (0x00007fff537ff000)
libacml_mv.so => not found
libacml.so => not found
libmpi.so => /opt/mpi/sgi/lib/libmpi.so (0x00007fe4444e8000)
libgfortran.so.3 => /usr/lib64/libgfortran.so.3 (0x00007fe44420e000)
libm.so.6 => /lib64/libm.so.6 (0x00007fe443fb8000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fe443da1000)
libc.so.6 => /lib64/libc.so.6 (0x00007fe443a43000)
/lib64/ld-linux-x86-64.so.2 (0x00007fe444817000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fe44383f000)
librt.so.1 => /lib64/librt.so.1 (0x00007fe443636000)
libcpuset.so.1 => /usr/lib64/libcpuset.so.1 (0x00007fe443429000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe44320c000)
libbitmask.so.1 => /usr/lib64/libbitmask.so.1 (0x00007fe443008000)
Unfortunately I am not the one who compiled the program and the guy who did is unreachable at the moment.
Thus, I do not have access to config.log right now, but I hope the above already gives some useful hint.
$ find / -iname 'config.log' 2> /dev/null
/opt/mpi/gnu/openmpi-1.10.2/share/vampirtrace/config.log
/opt/mpi/gnu/openmpi-1.6.5/share/vampirtrace/config.log
/opt/mpi/intel/openmpi-1.10.2/share/vampirtrace/config.log
/opt/mpi/intel/openmpi-1.6.5/share/vampirtrace/config.log
In case I get access to it I will report immediately.
Thank you for your time and help!
All the best,
Felipe
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Clicked A Few Times
Threads 4
Posts 13
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| 4:55:01 AM PST - Fri, Mar 3rd 2017 |
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It was a compilation problem.
It was recompiled and now it works properly.
Thanks for your time and effort.
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