Hi Lachele,
could you try different compiler?
Best,
Volodymyr
On Mon, May 10, 2010 16:23, Lachele Foley wrote:
> Sorry I've been quiet lately... very overwhelmed.
>
> A student did some testing, and she got a similar hang. For us, the hangs
> weren't random:
>
> ==============================================================
> make[2]: Leaving directory `/usr/local/amber11_20100507/test'
> cd neb-testcases/neb_gb_partial && ./Run.neb_gb_partial
>
> Running multisander version of sander Amber11
> Total processors = 4
> Number of groups = 4
> .......
>
> She said she tried it twice, and I confirmed it a third time just for fun.
> The serial tests went mostly well with 13 failures (all ncsu stuff) and
> one error (I think DFTB).
>
> Info of relevance (64-bit something?):
>
> Linux aarya.woods.ccrc 2.6.18-164.11.1.el5 #1 SMP Wed Jan 6 13:26:04 EST
> 2010 x86_64 x86_64 x86_64 GNU/Linux
>
> GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46)
>
> gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46)
>
> mpirun (Open MPI) 1.4.1
>
> mpicc -showme
> gcc -I/usr/local/include -pthread -L/usr/local/lib -lmpi -lopen-rte
> -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
>
> mpif90 -showme
> gfortran -I/usr/local/include -pthread -I/usr/local/lib -L/usr/local/lib
> -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic
> -lnsl -lutil -lm -ldl
>
> mpif77 -showme
> gfortran -I/usr/local/include -pthread -L/usr/local/lib -lmpi_f77 -lmpi
> -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
>
>
> She says she'll try on the machine in Ireland (64-bit with the wiggy file
> system), tonight.
>
> :-) Lachele
> --
> B. Lachele Foley, PhD '92,'02
> Assistant Research Scientist
> Complex Carbohydrate Research Center, UGA
> 706-542-0263
> lfoley.ccrc.uga.edu
>
>
> ----- Original Message -----
> From: Gustavo Seabra
> [mailto:gustavo.seabra.gmail.com]
> To: AMBER Developers Mailing List
> [mailto:amber-developers.ambermd.org]
> Sent: Mon, 10 May 2010 14:40:54
> -0400
> Subject: Re: [AMBER-Developers] sander.MPI tests randomly stall in
> Ubuntu 9.10
>
>
>> Hi,
>>
>> Here's what I have:
>> $ uname -a
>> Linux TIE1 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 14:05:01 UTC
>> 2009 x86_64 GNU/Linux
>>
>> $ gfortran --version
>> GNU Fortran (Ubuntu 4.4.1-4ubuntu9) 4.4.1
>>
>> $ gcc --version
>> gcc (Ubuntu 4.4.1-4ubuntu9) 4.4.1
>>
>> $ mpirun --version
>> mpirun (Open MPI) 1.3.2
>>
>> The serial version works just fine. I only see this with the parallel
>> version. The machine is a dual core AMD Athlon(tm) II X2 B22
>> Processor 800MHz, and I was running the tests with 4 mpi processes.
>>
>> Thanks,
>> Gustavo.
>>
>> On Fri, May 7, 2010 at 10:46 PM, Daniel Roe wrote:
>> > I personally havent seen this before. What compiler(s) are you using,
>> and
>> > what MPI implementation?
>> >
>> > -Dan
>> >
>> > On Fri, May 7, 2010 at 2:14 PM, Gustavo Seabra
>> <gustavo.seabra.gmail.com>wrote:
>> >
>> >> Hi All,
>> >>
>> >> I have compiled and tested Amber11 (release version) serial with no
>> >> problems on Ubuntu 9.10. Now, when I try the parallel version, it
>> >> compiles fine but some tests just stall. The processes keep running
>> >> (from "top" I can stil see the sander.MPI processes using all the
>> >> processor they need), but the calculation never advances.
>> >>
>> >> Which test will be a problem is random: I had with PIMD, then when I
>> >> try again it happens with QM tests, then something else, etc.
>> >>
>> >> I have found the following message on the archives:
>> >> http://structbio.vanderbilt.edu/archives/amber-archive/2009/5928.php
>> >>
>> >> But with no replies.
>> >>
>> >> Does anyone else experience such problems?
>> >>
>> >> Thanks,
>> >>
>> >> --
>> >> Gustavo Seabra
>>
>> _______________________________________________
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>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
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Received on Mon May 10 2010 - 16:00:05 PDT
