RE: AMBER: Compiling AMBER 8 for Mac OSX (Parallel)

From: Ross Walker <>
Date: Wed, 19 Jan 2005 10:23:40 -0800

Dear Emmanuel,

I trust you are using Amber 8.

> Unit 7 Error on OPEN: ^.^@^@^@.....
> [2] MPI Abort by user Aborting program !
> [2] Aborting program!

Unit 7 in sander is the mdinfo file which is not essential. What is
happening here is that the filename for the unit 7 file, which should be
'mdinfo' by default, is being corrupted when you run in parallel. This file
is opened by runmd.f at line 179 with the call:

If ( master ) call amopen(7,mdinfo,'U','F','W')

So, I suspect that the contents of mdinfo are being corrupted on the master
thread. Or alternatively threads other than the master are also calling
amopen. You can test that only one thread is the master and check the
contents of mdinfo by adding the line, above the if master:

Print *,master,mdinfo
If ( master ) call amopen(7,mdinfo,'U','F','W')

You should see 1 line for each process you are running. E.g. mpirun -np 4
should give you 4 lines. Only one line should have a True on it for the
master. All others should say F or False. For the mdinfo variable the thread
that has master = true should also have mdinfo set correctly. The other
threads will probably print garbage for mdinfo.

In your case, however, I suspect all threads will print garbage for the
mdinfo variable. Where and why it is getting corrupted, however, may take a
while to track down. Especially as I don't have a G5 available to me to test
it on.

Anyway, a quick fix you could try is to edit lines 177 and 179 of runmd.f
and change the mdinfo to 'mdinfo' - this will hardwire the filename to

So, the new lines should read:

if ( master ) call amopen(7,'mdinfo','U','F',facc)


if ( master ) call amopen(7,'mdinfo','U','F','W')

Then do

cd $AMBERHOME/src/
make clean
make parallel

Then try running the calculation again and see what happens.

I hope this helps,
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Wed Jan 19 2005 - 18:53:01 PST
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