AMBER Archive (2006)

Subject: Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband

From: Fabian Boes (
Date: Thu Jun 29 2006 - 12:53:23 CDT

Dear Bob,

> Are you sure you are not exceeding a file system size
>limit (say 2GB) for mdcrd or mdvel? Possibly file system
>quotas? Possibly full file systems? It would seem it
>almost has to be the file system, somehow, though I

The mdcrd should get not bigger than 180 MB within 50k
steps, as it is a rather small system. Some of the
filesystems i used had over 15 TB of free space, but i
will check for quotas.

>becomes unreachable in the middle of a run, everything
>should freeze up as you observe. I have mostly seen this
>kind of grief with Myrinet, but commodity clusters in
>general are not immune. We had a lot of trouble at unc
>for a while with our big infiniband p4 cluster with nodes
>becoming unreachable; I have no idea whether it was
>hardware burnin problems, config problems, loose

So, if PMEMD runs for some, lets say 5000, steps, with
resonable speed over Infiniband, then everything should be
OK with the compilation?

I will ask the guys at our computing center if they can
help me debugging with the Infiniband cards and/or

Thanks for your answer,

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