MPI + AMI mesh tutorial NOT working. tested anyone ?

Giuliano69 · September 14, 2012, 10:28

Hi,
we have a cluster of four WS, on which we positively run the motorbike tutorial on 16 cores. (MPI + nfs ver 3)
We had to downgrade nfs to version 3 to get things work, but with this parameter works flawlessly

Code:

/etc/fstab
192.168.0.17:/home/cfduser/OpenFOAM  /home/cfduser/OpenFOAM/  nfs _netdev,nfsvers=3,proto=tcp,noac,auto  0  0

But when we try the mixerVesselAMI2D case, the system gets stacked in createDynamicFvMesh.H. The main node get cpu% at 99% in sys time, and the slave get wait state at 100%, locked ....

Anyone have ever tried the tutorial with mixerVesselAMI2D MPI ?
Any idea what could lock the tutorial ?

wyldckat · September 15, 2012, 08:36

Hi Giuliano,

Bridging what we already know from your posts at http://www.cfd-online.com/Forums/ope...ple-nodes.html (posts #11 and 12), here's what I think might be responsible for all of this:

Server side of the NFS might be misconfigured for this task. Here's what we use at work:
Code:
```
fsid=0,crossmnt,rw,no_root_squash,sync,no_subtree_check
```
Caution: use "fsid" very carefully, or don't use it at all.

On the client side, we simply use the "defaults" option. openSUSE translates this to:

Code:

rw,relatime,vers=3,rsize=1048576,wsize=1048576,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,mountaddr=server_ip,mountvers=3,mountport=59044,mountproto=udp,local_lock=none,addr=server_ip

server_ip is the numerical IP address which I've erased when posting

I could see these options by running:

Code:

mount

According to your diagnosis, the lock up occurs right at a time when all machines go load the mesh files, possibly the same exact file. This is why I think something is misconfigured, given that it won't allow more than 2 machines to access the same file via NFS.

Right now I don't have access to the cluster resources at work, so I can't test this tutorial case myself. So I'll post again either when I access to more resources or I stumble on something else about NFS.

edit: Seems to me that Ubuntu 12.04 and NFS don't seem to play well together

: http://ubuntuforums.org/showthread.php?t=1478413

Best regards,
Bruno

PS: I moved this thread to where it seemed to fit better, namely in the "running" sub-forum.

Giuliano69 · October 12, 2012, 11:40

Thanks Bruno for you kind help.

I'm surprised to see that you use, "no_root_squash" . Are they diskless clients ?

man exports
root user on a client machine is also treated as root when accessing files on the NFS servehave you also tried nfs 4?

We found MPI perfomance very poor on nfs with XFS.
May I ask you which kind of filesystem are you using ?

Any parallel filesystem test ? :-)

Giuliano69 · October 12, 2012, 12:07

May I ask you a performance test ?

writing on a local directory I get 90Gb sec. We have all the 4 nodes on one HP switch 1910.

If I run
time dd bs=1M count=128 if=/dev/zero of=/home/cfduser/OpenFOAM/speedtest2 conv=fdatasync

I get a speed of 20 Gb/s
not so good, not so baad...

MAy I ask you your speed in your configuration ?

PS
conv=fdatasync gives real (longer) writing time, because wait for a write to end.

wyldckat · October 12, 2012, 16:47

Hi Giuliano,

Quote: