Am 10.11.2009 um 18:20 schrieb Eloi Gaudry:
Thanks for your help Reuti,
I'm using a nfs-shared directory (/opt/sge/tmp), exported from the
master node to all others computing nodes.
It's higly advisable to have the "tmpdir" local on each node. When
you use "cd $TMPDIR" in your jobscript, all is done local on a node
(when your application will just create the scratch file in your
current working directory) which will speed up the computation and
decrease the network traffic. Computing in as shared /opt/sge/tmp is
like computing in each user's home directory.
To avoid that any user can remove someone else's files, the "t" flag
is set like for /tmp: drwxrwxrwt 14 root root 4096 2009-11-10 18:35 /
tmp/
Nevertheless:
with for /etc/export on server (named moe.fft): /opt/sge
192.168.0.0/255.255.255.0(rw,sync,no_subtree_check)
/etc/fstab on
client: moe.fft:/opt/
sge /opt/sge
nfs rw,bg,soft,timeo=14, 0 0
Actually, the /opt/sge/tmp directory is 777 across all machines,
thus all user should be able to create a directory inside.
All access checkings will be applied:
- on the server: what is "ls -d /opt/sge/tmp" showing?
- the one from the export (this seems to be fine)
- the one on the node (i.e., how it's mounted: cat /etc/fstab)
The issue seems somehow related to the session directory created
inside /opt/sge/tmp, let's stay /opt/sge/tmp/29.1.smp8.q for
example for the job 29 on queue smp8.q. This subdirectory of /opt/
sge/tmp is created with nobody:nogroup drwxr-xr-x permissions...
which in turn forbids
Did you try to run some simple jobs before the parallel ones - are
these working? The daemons (qmaster and execd) were started as root?
The user is known on the file server, i.e. the machine hosting /opt/sge?
OpenMPI to create its subtree inside (as OpenMPI won't use
nobody:nogroup credentials).
In SGE the master process (the one running the job script) will
create the /opt/sge/tmp/29.1.smp8.q and also each started qrsh
inside SGE - all with the same name. What is your definition of the
PE in SGE which you use?
-- Reuti
Ad Ralph suggested, I checked the SGE configuration, but I haven't
found anything related to nobody:nogroup configuration so far.
Eloi
Reuti wrote:
Hi,
Am 10.11.2009 um 17:55 schrieb Eloi Gaudry:
Thanks for your help Ralph, I'll double check that.
As for the error message received, there might be some
inconsistency: "/opt/sge/tmp/25.1.smp8.q/openmpi-sessions-
eg@charlie_0" is the
often /opt/sge is shared across the nodes, while the /tmp
(sometimes implemented as /scratch in a partition on its own)
should be local on each node.
What is the setting of "tmpdir" in your queue definition?
If you want to share /opt/sge/tmp, everyone must be able to write
into this location. As for me it's working fine (with the local /
tmp), I assume the nobody/nogroup comes from any squash-setting in
the /etc/export of you master node.
-- Reuti
parent directory and "/opt/sge/tmp/25.1.smp8.q/openmpi-sessions-
eg@charlie_0/53199/0/0" is the subdirectory... not the other way
around.
Eloi
Ralph Castain wrote:
Creating a directory with such credentials sounds like a bug in
SGE to me...perhaps an SGE config issue?
Only thing you could do is tell OMPI to use some other directory
as the root for its session dir tree - check "mpirun -h", or
ompi_info for the required option.
But I would first check your SGE config as that just doesn't
sound right.
On Nov 10, 2009, at 9:40 AM, Eloi Gaudry wrote:
Hi there,
I'm experiencing some issues using GE6.2U4 and OpenMPI-1.3.3
(with gridengine compnent).
During any job submission, SGE creates a session directory in
$TMPDIR, named after the job id and the computing node name.
This session directory is created using nobody/nogroup
credentials.
When using OpenMPI with tight-integration, opal creates
different subdirectories in this session directory. The issue
I'm facing now is that OpenMPI fails to create these
subdirectories:
[charlie:03882] opal_os_dirpath_create: Error: Unable to create
the sub-directory (/opt/sge/tmp/25.1.smp8.q/openmpi-sessions-
eg@charlie_0) of (/opt/sge/tmp/25.1.smp8.q/openmpi-sessions-
eg@charlie_0
[charlie:03882] [[53199,0],0] ORTE_ERROR_LOG: Error in
file ../../openmpi-1.3.3/orte/util/session_dir.c at line 101
[charlie:03882] [[53199,0],0] ORTE_ERROR_LOG: Error in
file ../../openmpi-1.3.3/orte/util/session_dir.c at line 425
[charlie:03882] [[53199,0],0] ORTE_ERROR_LOG: Error in
file ../../../../../openmpi-1.3.3/orte/mca/ess/hnp/
ess_hnp_module.c at line 273
------------------------------------------------------------------
--------
It looks like orte_init failed for some reason; your parallel
process is
likely to abort. There are many reasons that a parallel
process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal
failure;
here's some additional information (which may only be relevant
to an
Open MPI developer):
orte_session_dir failed
--> Returned value Error (-1) instead of ORTE_SUCCESS
------------------------------------------------------------------
--------
[charlie:03882] [[53199,0],0] ORTE_ERROR_LOG: Error in
file ../../openmpi-1.3.3/orte/runtime/orte_init.c at line 132
------------------------------------------------------------------
--------
It looks like orte_init failed for some reason; your parallel
process is
likely to abort. There are many reasons that a parallel
process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal
failure;
here's some additional information (which may only be relevant
to an
Open MPI developer):
orte_ess_set_name failed
--> Returned value Error (-1) instead of ORTE_SUCCESS
------------------------------------------------------------------
--------
[charlie:03882] [[53199,0],0] ORTE_ERROR_LOG: Error in
file ../../../../openmpi-1.3.3/orte/tools/orterun/orterun.c at
line 473
This seems very likely related to the permissions set on $TMPDIR.
I'd like to know if someone might have experienced the same or
a similar issue and if any solution was found.
Thanks for your help,
Eloi
--
Eloi Gaudry
Free Field Technologies
Axis Park Louvain-la-Neuve
Rue Emile Francqui, 1
B-1435 Mont-Saint Guibert
BELGIUM
Company Phone: +32 10 487 959
Company Fax: +32 10 454 626
_______________________________________________
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
_______________________________________________
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
--
Eloi Gaudry
Free Field Technologies
Axis Park Louvain-la-Neuve
Rue Emile Francqui, 1
B-1435 Mont-Saint Guibert
BELGIUM
Company Phone: +32 10 487 959
Company Fax: +32 10 454 626
_______________________________________________
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
_______________________________________________
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
--
Eloi Gaudry
Free Field Technologies
Axis Park Louvain-la-Neuve
Rue Emile Francqui, 1
B-1435 Mont-Saint Guibert
BELGIUM
Company Phone: +32 10 487 959
Company Fax: +32 10 454 626
_______________________________________________
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
