Hi Reuti,
I followed your advice and switched to a local "tmpdir" instead of a
share one. This solved the session directory issue, thanks for your help !
However, I cannot understand how the issue disappeared. Any input would
be welcome as I really like to understand how SGE/OpenMPI could failed
when using such a configuration (i.e. with a shared "tmpdir").
Eloi
On 10/11/2009 19:17, Eloi Gaudry wrote:
Reuti,
The acl here were just added when I tried to force the /opt/sge/tmp
subdirectories to be 777 (which I did when I first encountered the
error of subdirectories creation within OpenMPI). I don't think the
info I'll provide will be meaningfull here:
moe:~# getfacl /opt/sge/tmp
getfacl: Removing leading '/' from absolute path names
# file: opt/sge/tmp
# owner: sgeadmin
# group: fft
user::rwx
group::rwx
mask::rwx
other::rwx
default:user::rwx
default:group::rwx
default:group:fft:rwx
default:mask::rwx
default:other::rwx
I'll try to use a local directory instead of a shared one for
"tmpdir". But as this issue seems somehow related to permissions, I
don't know if this would eventually be the rigth solution.
Thanks for your help,
Eloi
Reuti wrote:
Hi,
Am 10.11.2009 um 19:01 schrieb Eloi Gaudry:
Reuti,
I'm using "tmpdir" as a shared directory that contains the session
directories created during job submission, not for computing or
local storage. Doesn't the session directory (i.e.
job_id.queue_name) need to be shared among all computing nodes (at
least the ones that would be used with orted during the parallel
computation) ?
no. orted runs happily with local $TMPDIR on each and every node. The
$TMPDIRs are intended to be used by the user for any temporary data
for his job, as they are created and removed by SGE automatically for
every job for his convenience.
All sequential job run fine, as no write operation is performed in
"tmpdir/session_directory".
All users are known on the computing nodes and the master node (with
use ldap authentication on all nodes).
As for the access checkings:
moe:~# ls -alrtd /opt/sge/tmp
drwxrwxrwx+ 2 sgeadmin fft 4096 2009-11-10 18:28 /opt/sge/tmp
Aha, the + tells that there are some ACLs set:
getfacl /opt/sge/tmp
And for the parallel environment configuration:
moe:~# qconf -sp round_robin
pe_name round_robin
slots 32
user_lists NONE
xuser_lists NONE
start_proc_args /bin/true
stop_proc_args /bin/true
allocation_rule $round_robin
control_slaves TRUE
job_is_first_task FALSE
urgency_slots min
accounting_summary FALSE
Okay, fine.
-- Reuti
Thanks for your help,
Eloi
Reuti wrote:
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
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