AMBER Archive (2009)

Subject: Re: [AMBER] pmemd compile error....

From: Yiannis Georgiadis (giannis_at_cc.uoa.gr)
Date: Tue Mar 24 2009 - 15:10:27 CDT

Dear Bob

I didn't managed to run uniprocessor sander nor pmemd
sander gives segmentation fault and pmemd is stopped with
"STOP PMEMD Terminated Abnormally"
a message existed in pmemd_lib.f90 code

I found references on segmentation fault runnings
when we call c routines from fortran
as http://docs.hp.com/en/B3909-90002/ch04s05.html says

any suggestion ?

Yiannis Georgiadis

Robert Duke wrote:
> Hmmm. Insufficient information. For some reason, mpi initialization
> seems to be failing in the 7th task. This may be a myriad of things,
> but I would tend to suspect some sort of library or compilation
> problems. If I were dealing with this personally, I would do the
> following:
> 1) Take a known simple testcase - say the JACS benchmark.
> 2) Compile the uniprocessor version of pmemd and run it on this
> machine - any problems?
> 3) If not, compiler sander or mpi test code on this beast - does
> sander run the problem okay? There could be all kinds of
> "interesting" library and mpi issues.
> 4) If all that works, recompile parallel pmemd, but set F90_OPT_DFLT
> to $(F90_OPT_DBG). This may give you a coredump from which you can
> get more info.
>
> It looks to me like you are not even getting through mpi
> initialization here, which basically says it is not a pmemd problem,
> per se, but something about how you are compiling/linking in this
> environment. I really don't know though, given the limited info.
>
> Oh one thing. You say you "recompiled with 64bit compiler because the
> HP supercomputer has more than 1 GB stack limit". Okay, BAD move.
> You absolutely don't want to be matching 32 and 64 bit code unless the
> mixing is supported by the libraries, and generally there are
> libraries that will be used for a 32 or 64 bit executable. You simply
> can't get into memory problems with pmemd on a 32 bit executable with
> more than say 4 processors, and it costs typically at least 5% to go
> into 64 bit mode due to the expansion of code/data associated with the
> use of 64 bit instead of 32 bit pointers. So if you dinked with the
> build params, undink. The pmemd code works on some systems with a 64
> bit build (like ibm aix) but it is slower, and tricky to get linked
> right, and can die in various nasty hard to diagnose ways. So "64-bit
> good, 32-bit bad, is highly faulty logic". It is only good to use 64
> bits if you have massive amounts of data, and you don't. Attached is a
> graphic showing resident memory requirements of pmemd (on 4
> processors), and the stack memory is a small fraction of the total
> memory used. And note, you can't run problems larger than 999,999
> atoms with pmemd, but that is a file format problem, not a memory
> usage problem. Now you CAN get into memory problems with pmemd, but
> it requires 1) running on 1 or a very few processors, 2) using a
> really large problem - multiple 100's of thousands of atoms, AND 3)
> setting the cutoff to something like half the boxsize - then the
> pairlist will be just huge, and you can blow up on that. Be sure to
> use an 8 or 9 angstrom cutoff in pmemd running pme - very little in
> the way of good reasons to do otherwise.
>
> Hope this helps - Bob Duke
> (getting any new system up that has not been previously configured can
> be sort of a pain - sorry)
>
> ----- Original Message ----- From: "Giorgos Lamprinidis"
> <lamprinidis_at_pharm.uoa.gr>
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Sent: Thursday, March 19, 2009 11:06 AM
> Subject: [AMBER] pmemd compile error....
>
>
> Duke,
>
>
>
> My colleague Giannis Georgiadis re-compiled pmemd with 64bit compiler
> because our HP supercomputer has more than 1GB stack limit for 64bit
> applications. We shall increase the stack limit for the 32bit version
> to 400MB (this is the maximum) when he reboot the computer.
>
> The warning messages disappeared but the Terminated Abnormally errors
> are still there without any other messages..
>
> ...................
>
> STOP PMEMD Terminated Abnormally!
>
> STOP PMEMD Terminated Abnormally!
>
> STOP PMEMD Terminated Abnormally!
>
> STOP PMEMD Terminated Abnormally!
>
> STOP PMEMD Terminated Abnormally!
>
> STOP PMEMD Terminated Abnormally!
>
> STOP PMEMD Terminated Abnormally!
>
> STOP PMEMD Terminated Abnormally!
>
> MPI Application rank 6 exited before MPI_Init() with status 0
>
> Failed sending message: (Unable to connect to socket (Connection
> refused)).
>
> ....................
>
>
>
> Any suggestions plz?
>
>
>
> Dr George Lamprinidis
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