Hello Alexei,

I can pass the environment variables using mpirun.ch_gm command. Do you
mean I would need to pass all of SCM_VECTORLENGTH, SCM_WD, SCM_IOBUFFERSIZE,
SCM_DIAG_EXCLUDE, SCM_DEBUG, SCM_NEWDIAG, SCM_TMPDIR, SCM_USETMPDIR,
SCM_NOMEMCHECK, and SCMLICENSE, SCM_STDIN? I know the variable SCM_WD must
be passed due to the "/bin/cp: omitting directory" error. Could you tell
me which variable I will need to pass and what is the value of the
variable I need to use?

Thanks for your help.

Yiye

On Tue, 16 Aug 2005, Alexei Yakovlev wrote:

> Dear Dr. Huang,
>
> These error messages usually indicate that environment variables are not
> passed from mpirun to the ADF master node. Whether variables are passed
> or not depends on the MPI implementation and can sometimes be influenced
> by mpirun switches. From my experience, the mpirun command that comes
> with MPICH (ch_p4) only passes environment if the master node is spawned
> directly by mpirun and not via ssh/rsh. The latter happens when one is
> using -nolocal. As far as I know, ch_gm has a command line option to
> request passing of certain environment variables from mpirun to the
> executed program. For example, to pass two variable FOO_1 and FOO_2 to a
> parallel program use the following command option (from
> http://www.myri.com/scs/READMES/README-mpich-gm):
> mpirun FOO_1=<my_value_there> FOO_2=<another_value> -np 2 foo.x
>
> For ADF, the most important environment variables are SCM_VECTORLENGTH,
> SCM_WD, SCM_IOBUFFERSIZE, SCM_DIAG_EXCLUDE, SCM_DEBUG, SCM_NEWDIAG,
> SCM_TMPDIR, SCM_USETMPDIR, SCM_NOMEMCHECK, and SCMLICENSE, SCM_STDIN.
>
> In the next version, we've implemented a permanent solution. All
> necessary environment variables can be passed to ADF on the command line
> as -DNAME=value. We hope this solution will work in all cases.
>
> Best regards,
> Alexei
>
>
> Y. Huang wrote:
>
> >Hello,
> >
> >I am running ADF jobs on a dual Opteron cluster connected by Myrinet
> >interconnect. OS is SuSE. MPICH-GM has been installed on the system. I
> >have set the following environment variables in .bashrc
> >
> >export ADFHOME=/home/huang/software/ADF/adf2004.01
> >export ADFBIN=$ADFHOME/bin
> >export ADFRESOURCES=$ADFHOME/atomicdata
> >export SCMLICENSE=$ADFHOME/license
> >export MPIDIR=/opt/mpigm
> >export SCM_MACHINEFILE=/home/huang/nodes
> >export NSCM=4
> >export SCM_TMPDIR=/tmp
> >export SCM_USETMPDIR=yes
> >export P4_RSHCOMMAND=/usr/bin/ssh
> >
> >The file /home/huang/nodes contains 4 nodes.
> >
> >I got the following errors when I ran the example accompanied with the ADF
> >package in the directory of examples/adf/e_AIM_HF:
> >
> >...
> >/bin/cp: omitting directory `/dev'
> >/bin/cp: omitting directory `/etc'
> >/bin/cp: omitting directory `/home'
> >/bin/cp: omitting directory `/lib'
> >/bin/cp: omitting directory `/lib64'
> >/bin/cp: omitting directory `/lost+found'
> >/bin/cp: omitting directory `/media'
> >/bin/cp: omitting directory `/mnt'
> >/bin/cp: omitting directory `/opt'
> >/bin/cp: omitting directory `/opt.orig'
> >/bin/cp: omitting directory `/proc'
> >/bin/cp: omitting directory `/root'
> >/bin/cp: omitting directory `/sbin'
> >/bin/cp: omitting directory `/srv'
> >/bin/cp: omitting directory `/sys'
> >/bin/cp: omitting directory `/tmp'
> >/bin/cp: omitting directory `/usr'
> >/bin/cp: omitting directory `/var'
> >...
> > <Aug15-2005> <11:56:10> ADF 2004.01 RunTime: Aug15-2005 11:56:10
> > <Aug15-2005> <11:56:10> *** (NO TITLE) ***
> > <Aug15-2005> <11:56:10> RunType : SINGLE POINT
> > <Aug15-2005> <11:56:10> NO ATOMS INPUT
> > <Aug15-2005> <11:56:10> ardel: last array to be deleted not found
> > <Aug15-2005> <11:56:10> NO ATOMS INPUT
> > <Aug15-2005> <11:56:10> END
> >ERROR DETECTED
> > ************* Input file not found *************
> >KFEXIT
> >Contents of rdt21.res:
> >cat: rdt21.res: No such file or directory
> >Contents of WFN-alpha:
> >cat: WFN-alpha: No such file or directory
> >Contents of WFN-beta:
> >cat: WFN-beta: No such file or directory
> >
> >
> >Any suggestion is appreciated.
> >
> >Yiye
> >
> >**********************************
> > Faculty of Science
> > University of Waterloo
> > Waterloo, Ontario N2L 3G1
> > E-mail: huang_at_uwaterloo.ca
> > Tel: (519) 888-4567 ext.6110
> >**********************************
> >| (\
> >| http://hpc.uwaterloo.ca ( \
> >|__________________________) ) />
> > / ) / //))/
> > \ \_/ /////
> > \ /
> > \_ /
> > | |
> > |___|
> >
> >
> >
> >
>
Received on 2005-08-16 16:21:49