Dear Amber-users,
I successfully patched, configured, compiled/installed Amber Tools 1.2 and
Amber 10 (serial and parallel) including pmemd
without any problems !
Here are just my configuration commands:
./configure_at icc
./configure_amber ifort (for amber serial)
./configure_amber -intelmpi ifort (for amber parallel)
./configure linux_em64t ifort intelmpi pubfft bintraj (for pmemd)
Then I started the reccomended tests in dir amber/test
make test.serial
make test.parallel
make test.serial.QMMM
make test.parallel.QMMM
Lot of tests passed without problems, but
unfortunatelly not all of them.
In the case of "make test.serial" and "make test.parallel" I obtained
error:
--------------------------------------
MLK func load error: /opt/intel/mkl/10.0.011/lib/em64t/libmkl_vml_mc.so:
undefined symbol: vmlGetErrorCallBack
./Run.circdna: Program error
make: *** [test.sander.GB] Error 1
------------------------------------
In the case of "make test.serial.QMMM" and "make test.parallel.QMMM" it
was similar error:
----------------------------------------
MLK func load error: /opt/intel/mkl/10.0.011/lib/em64t/libmkl_vml_mc.so:
undefined symbol: vmlGetErrorCallBack
./Run.1NLN_internal: Program error
make: *** [test.sander.QMMM] Error 1
----------------------------------------
The problem is the same in both cases "undefined symbol:
vmlGetErrorCallBack". In the first case "circdna" it is caused
by setting igb=1. If igb=0 it is everything OK. So it means that in the
case of minimisation in implicit solvent sander
is attempting to use MKL but from some strange reason he is not able to do
it. I am not an expert but I think that all the necessary env. variables
are set properly - please see the "env list" below.
I saw just a few similar emails in Amber mail-list but without
satisfactory explanation.
The suggestions was:
#1 - to use static compilation
#2 - not to use MKL
So first of all I would really prefare to know what is the root of my
problem. So I am kindly asking some experts to check
my environment setting (ENV LIST) if everything is OK there, if for
example all the important MKL paths are set ...
If there is no problem from the "PATHS" point of view. What could be other
possible cause/s ?
I have just one idea - proper instalation of MKL (this was done by
maintenance person not by me). If this could be
the case it is some easy way how to check MKL instalation - for example to
run some tests like in AMBER ?
Any ideas are highly appreciated !
------ENV LIST-------------------------
MANPATH=/opt/intel/mkl/10.0.011/man:/opt/intel/mkl/10.0.011/man:/opt/intel/cce/9.1.043/man:/opt/intel/fce/10.1.012/man:/usr/local/share/man:/usr/share/man:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.16.1/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.1/man
INTEL_LICENSE_FILE=/opt/intel/fce/10.1.012/licenses:/opt/intel/licenses:/home/mmaly/intel/licenses:/Users/Shared/Library/Application
Support/Intel/Licenses:/opt/intel/cce/9.1.043/licenses:/opt/intel/licenses:/home/mmaly/intel/licenses
TERM=xterm
SHELL=/bin/bash
SSH_CLIENT=192.168.0.128 35559 22
LIBRARY_PATH=/opt/intel/mkl/10.0.011/lib/em64t:/opt/intel/mkl/10.0.011/lib/em64t
FPATH=/opt/intel/mkl/10.0.011/include:/opt/intel/mkl/10.0.011/include
OLDPWD=/home/mmaly/_applications/amber/test
SSH_TTY=/dev/pts/0
USER=mmaly
LD_LIBRARY_PATH=/opt/intel/mkl/10.0.011/lib/em64t:/opt/intel/impi/3.1/lib64:/opt/intel/mkl/10.0.011/lib/em64t:/opt/intel/cce/9.1.043/lib:/opt/intel/fce/10.1.012/lib::/opt/intel/impi/3.1/lib64
LS_COLORS=no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41: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:*.zip=01;31:*.z=01;31:*.Z=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:*.mng=01;35:*.pcx=01;35:*.yuv=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:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.pdf=00;32:*.ps=00;32:*.txt=00;32:*.patch=00;32:*.diff=00;32:*.log=00;32:*.tex=00;32:*.doc=00;32
:*.flac=01;35:*.mp3=01;35:*.mpc=00;36:*.ogg=00;36:*.wav=00;36:*.mid=00;36:*.midi=00;36:*.au=00;36:*.flac=00;36:*.aac=00;36:*.ra=01;36:*.mka=01;36:
SGE_HOME=/opt/sge/amd64
CPATH=/opt/intel/mkl/10.0.011/include:/opt/intel/mkl/10.0.011/include
PAGER=/usr/bin/less
CONFIG_PROTECT_MASK=/etc/fonts/fonts.conf /etc/terminfo
MAIL=/var/mail/mmaly
PATH=/opt/intel/impi/3.1/bin64:/opt/intel/cce/9.1.043/bin:/opt/intel/fce/10.1.012/bin:/usr/local/bin:/usr/bin:/bin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.1.1:/opt/intel/cce/9.1.043/bin:/opt/intel/fce/10.1.012/bin:/opt/intel/impi/3.1/bin:/opt/intel/idbe/9.1.043/bin:/opt/intel/idbe/10.1.012/bin:/opt/intel/etc:/opt/amber/exe:/opt/sge/amd64/bin
PWD=/home/mmaly/_applications/amber/test/circ_dna
EDITOR=/bin/nano
MKL_HOME=/opt/intel/mkl/10.0.011
INTEL_PATHS=/opt/intel/cce/9.1.043/bin:/opt/intel/fce/10.1.012/bin:/opt/intel/impi/3.1/bin:/opt/intel/idbe/9.1.043/bin:/opt/intel/idbe/10.1.012/bin:/opt/intel/etc
SHLVL=1
HOME=/home/mmaly
DYLD_LIBRARY_PATH=/opt/intel/fce/10.1.012/lib
PYTHONPATH=/usr/lib64/portage/pym
LESS=-R -M --shift 5
LOGNAME=mmaly
GCC_SPECS=
CVS_RSH=ssh
SSH_CONNECTION=192.168.0.128 35559 192.168.0.12 22
MPI_HOME=/opt/intel/impi/3.1
LESSOPEN=|lesspipe.sh %s
INFOPATH=/usr/share/info:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.16.1/info:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.1/info:/usr/share/info/emacs-22
INCLUDE=/opt/intel/mkl/10.0.011/include:/opt/intel/mkl/10.0.011/include
AMBERHOME=/opt/amber
_=/usr/bin/env
In the case of "bypass" solution #1 what should be compiled statically
A.Tools+Amber or Amber is enough ? In the case
of Amber - pmemd for example doesn't -static flag allowed so it is OK to
compile Amber by static way and pmemd not ?
Anyway I do not understand much why after static linking (including MKL
libraries) should solve my problem with
"undefined symbol: vmlGetErrorCallBack" but OK I will try it if necessary.
If I do not succeed there is probably just
the #2 solution. So to this point I have just one question. How to do it ?
It is enough to delete any "MKL records"
which are automatically generated into header files "config.h" and
"config_amber.h" ?
So again thanks very much in advance for any info which can help me to
find out the cause of the above error or at least
for some additional info regarding to that two "bypass" solutions.
Marek
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
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Received on Wed Feb 04 2009 - 01:35:37 PST
