Re: [AMBER] amber installation test question

From: James Kress <>
Date: Sun, 29 Jan 2017 15:51:48 -0500


Thanks for the reply.

Please be careful with OpenMPI 2.0.1 The OpenMPI mailing list is full of
posts where problems have been found with 2.0.1.


-----Original Message-----
From: David Case []
Sent: Saturday, January 28, 2017 8:48 PM
To:; AMBER Mailing List <>
Subject: Re: [AMBER] amber installation test question

On Sat, Jan 28, 2017, James Kress wrote:

> I tried openMPI 1.6.5 and ran the tests, again. They ran but with one
> error that I do not understand.
> cd nfe && ./
> /bin/sh: ./ Permission denied

This is our fault, with incorrect permissions. It will be fixed in the next
release, and is not a cause for concern.

Note however, the the "noboxinfo" test you reported earlier is only run for
sander, not for pmemd. The log file you attached was for pmemd. You might
look at the AmberTools test logfile to search for "noboxinfo", to see if the
test indeed PASSED with openMPI 1.6.5. (I'm guessing that it did, since
otherwise you would have seen the hang reported earlier; but it's probably
best to make sure.)

update: I can confirm the report of a hang when using openmpi-1.10.5; the
test passes with the current openmpi-2.0.1. I haven't been able to see
anything suspicious about the code involved (although others could look).
But given that both earlier and later versions of openmpi work as expected,
I think for the moment we will just recommend not using 1.10.


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Received on Sun Jan 29 2017 - 13:00:02 PST
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