Hi Beichuan
OK, it says "unclassified.html", so I presume it is not a problem.
The web site says the computer is an SGI ICE X.
I am not familiar to it, so what follows are guesses.
The SGI site brochure suggests that the nodes/blades have local disks:
https://www.sgi.com/pdfs/4330.pdf
The file systems prefixed with IP addresses (work[1-4]) and
with panfs (cwfs and CWFS[1-6]) and a colon (:)
are shared exports (not local), but not necessarily NFS (panfs may be
Panasas?).
From this output it is hard to tell where /home is, but I would guess
it is also shared (not local).
Maybe "df -h /home" will tell. Or perhaps "mount".
You may be logged in to a login/service node, so
although it does have a /tmp (your ls / shows tmp),
this doesn't guarantee that the compute nodes/blades also do.
Since your jobs failed when you specified TMPDIR=/tmp,
I would guess /tmp doesn't exist on the nodes/blades,
or is not writable.
Did you try to submit a job with, say, "mpiexec -np 16 ls -ld /tmp"?
This should tell if /tmp exists on the nodes, if it is writable.
A stupid question:
When you tried your job with this:
export TMPDIR=/home/yanb/tmp
Did you create the directory /home/yanb/tmp beforehand?
Anyway, you may need to ask the help of a system administrator of this
machine.
Gus Correa
On 03/03/2014 07:43 PM, Beichuan Yan wrote:
Gus,
I am using this system: http://centers.hpc.mil/systems/unclassified.html#Spirit. I don't
know exactly configurations of the file system. Here is the output of "df -h":
Filesystem Size Used Avail Use% Mounted on
/dev/sda6 919G 16G 857G 2% /
tmpfs 32G 0 32G 0% /dev/shm
/dev/sda5 139M 33M 100M 25% /boot
adfs3v-s:/adfs3/hafs14
6.5T 678G 5.5T 11% /scratch
adfs3v-s:/adfs3/hafs16
6.5T 678G 5.5T 11% /var/spool/mail
10.148.18.45@o2ib:10.148.18.46@o2ib:/fs1
1.2P 136T 1.1P 12% /work1
10.148.18.132@o2ib:10.148.18.133@o2ib:/fs4
1.2P 793T 368T 69% /work4
10.148.18.104@o2ib:10.148.18.165@o2ib:/fs3
1.2P 509T 652T 44% /work3
10.148.18.76@o2ib:10.148.18.164@o2ib:/fs2
1.2P 521T 640T 45% /work2
panfs://172.16.0.10/CWFS
728T 286T 443T 40% /p/cwfs
panfs://172.16.1.61/CWFS1
728T 286T 443T 40% /p/CWFS1
panfs://172.16.0.210/CWFS2
728T 286T 443T 40% /p/CWFS2
panfs://172.16.1.125/CWFS3
728T 286T 443T 40% /p/CWFS3
panfs://172.16.1.224/CWFS4
728T 286T 443T 40% /p/CWFS4
panfs://172.16.1.224/CWFS5
728T 286T 443T 40% /p/CWFS5
panfs://172.16.1.224/CWFS6
728T 286T 443T 40% /p/CWFS6
panfs://172.16.1.224/CWFS7
728T 286T 443T 40% /p/CWFS7
1. My home directory is /home/yanb.
My simulation files are located at /work3/yanb.
The default TMPDIR set by system is just /work3/yanb
2. I did try not to set TMPDIR and let it default, which is just case 1 and
case 2.
Case1: #export TMPDIR=/home/yanb/tmp
TCP="--mca btl_tcp_if_include 10.148.0.0/16"
It gives no apparent reason.
Case2: #export TMPDIR=/home/yanb/tmp
#TCP="--mca btl_tcp_if_include 10.148.0.0/16"
It gives warning of shared memory file on network file system.
3. With "export TMPDIR=/tmp", the job gives the same, no apparent reason.
4. FYI, "ls /" gives:
ELT apps cgroup hafs1 hafs12 hafs2 hafs5 hafs8 home
lost+found mnt p root selinux tftpboot var work3
admin bin dev hafs10 hafs13 hafs3 hafs6 hafs9 lib media
net panfs sbin srv tmp work1 work4
app boot etc hafs11 hafs15 hafs4 hafs7 hafs_x86_64 lib64 misc
opt proc scratch sys usr work2 workspace
Beichuan
-----Original Message-----
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Monday, March 03, 2014 17:24
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
Hi Beichuan
If you are using the university cluster, chances are that /home is not local,
but on an NFS share, or perhaps Lustre (which you may have mentioned before, I
don't remember).
Maybe "df -h" will show what is local what is not.
It works for NFS, it prefixes file systems with the server name, but I don't
know about Lustre.
Did you try just not to set TMPDIR and let it default?
If the default TMPDIR is on Lustre (did you say this?, anyway I don't
remember) you could perhaps try to force it to /tmp:
export TMPDIR=/tmp,
If the cluster nodes are diskfull /tmp is likely to exist and be local to the
cluster nodes.
[But the cluster nodes may be diskless ... :( ]
I hope this helps,
Gus Correa
On 03/03/2014 07:10 PM, Beichuan Yan wrote:
How to set TMPDIR to a local filesystem? Is /home/yanb/tmp a local filesystem?
I don't know how to tell a directory is local file system or network file
system.
-----Original Message-----
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Jeff
Squyres (jsquyres)
Sent: Monday, March 03, 2014 16:57
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
How about setting TMPDIR to a local filesystem?
On Mar 3, 2014, at 3:43 PM, Beichuan Yan<beichuan....@colorado.edu> wrote:
I agree there are two cases for pure-MPI mode: 1. Job fails with no apparent reason; 2
job complains shared-memory file on network file system, which can be resolved by "
export TMPDIR=/home/yanb/tmp", /home/yanb/tmp is my local directory. The default
TMPDIR points to a Lustre directory.
There is no any other output. I checked my job with "qstat -n" and found that processes
were actually not started on compute nodes even though PBS Pro has "started" my job.
Beichuan
3. Then I test pure-MPI mode: OPENMP is turned off, and each compute node runs 16 processes
(clearly shared-memory of MPI is used). Four combinations of "TMPDIR" and "TCP"
are tested:
case 1:
#export TMPDIR=/home/yanb/tmp
TCP="--mca btl_tcp_if_include 10.148.0.0/16"
mpirun $TCP -np 64 -npernode 16 -hostfile $PBS_NODEFILE
./paraEllip3d input.txt
output:
Start Prologue v2.5 Mon Mar 3 15:47:16 EST 2014 End Prologue v2.5
Mon Mar 3 15:47:16 EST 2014
-bash: line 1: 448597 Terminated
/var/spool/PBS/mom_priv/jobs/602244.service12.SC
Start Epilogue v2.5 Mon Mar 3 15:50:51 EST 2014 Statistics
cpupercent=0,cput=00:00:00,mem=7028kb,ncpus=128,vmem=495768kb,wallti
m
e
=00:03:24 End Epilogue v2.5 Mon Mar 3 15:50:52 EST 2014
It looks like you have two general cases:
1. The job fails for no apparent reason (like above), or 2. The job
complains that your TMPDIR is on a shared filesystem
Right?
I think the real issue, then, is to figure out why your jobs are failing with
no output.
Is there anything in the stderr output?
--
Jeff Squyres
jsquy...@cisco.com
For corporate legal information go to:
http://www.cisco.com/web/about/doing_business/legal/cri/
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--
Jeff Squyres
jsquy...@cisco.com
For corporate legal information go to:
http://www.cisco.com/web/about/doing_business/legal/cri/
_______________________________________________
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
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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
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http://www.open-mpi.org/mailman/listinfo.cgi/users
