Re: NAMD2.6b2: Segmentation fault

From: Morad Alawneh (alawneh_at_chem.byu.edu)
Date: Tue Aug 22 2006 - 10:05:42 CDT

Thanks for your comments.

Since there is no difference between the two versions, I think the
problem is in the hardware of this system. Specially, when only one job
of mine is running that means my compilation is fine.

Thanks

/*Morad Alawneh*/

*Department of Chemistry and Biochemistry*

*C100 BNSN, BYU*

*Provo, UT 84602*

Jim Phillips wrote:
>
> I can't tell much from just a segfault. Does the charm++ megatest
> work? Does NAMD run on one processor? Is there *any* output at all?
>
> My only comments looking at your build script are that on the charm
> ./build line "-language charm++ -balance rand" shouldn't be needed and
> may be harmful. Also, you shouldn't need "CHARMOPTS = -thread
> pthreads -memory os" with the TopSpin MPI library. It looks like
> you're following
> http://www.ks.uiuc.edu/Research/namd/wiki/?NamdOnInfiniBand but using
> the VMI build instructions. Also, please use the charm-5.9 source
> distributed with the NAMD source code, since this is the stable tree.
>
> -Jim
>
>
> On Mon, 21 Aug 2006, Morad Alawneh wrote:
>
>> Dear users,
>>
>> I have installed successfully NAMD2.6b1 onto my system, the installation
>> instructions are attached with this email, and the program was working
>> without any problem.
>>
>> I followed the same way for installing NAMD2.6b2, but after submitting a
>> job I received the following message in the error log file:
>>
>> bash: line 1: 31904 Segmentation fault /usr/bin/env MPIRUN_MPD=0
>> MPIRUN_HOST=m4a-7-11.local MPIRUN_PORT=40732
>> MPIRUN_PROCESSES='m4a-7-11i:m4a-7-11i:m4a-7-11i:m4a-7-11i:m4a-7-10i:m4a-7-10i:m4a-7-10i:m4a-7-10i:m4a-7-9i:m4a-7-9i:m4a-7-9i:m4a-7-9i:m4a-7-8i:m4a-7-8i:m4a-7-8i:m4a-7-8i:m4a-7-7i:m4a-7-7i:m4a-7-7i:m4a-7-7i:m4a-7-6i:m4a-7-6i:m4a-7-6i:m4a-7-6i:m4a-7-5i:m4a-7-5i:m4a-7-5i:m4a-7-5i:m4a-7-4i:m4a-7-4i:m4a-7-4i:m4a-7-4i:m4a-6-24i:m4a-6-24i:m4a-6-24i:m4a-6-24i:m4a-6-23i:m4a-6-23i:m4a-6-23i:m4a-6-23i:m4a-6-22i:m4a-6-22i:m4a-6-22i:m4a-6-22i:m4a-6-21i:m4a-6-21i:m4a-6-21i:m4a-6-21i:m4a-6-20i:m4a-6-20i:m4a-6-20i:m4a-6-20i:m4a-6-19i:m4a-6-19i:m4a-6-19i:m4a-6-19i:m4a-6-18i:m4a-6-18i:m4a-6-18i:m4a-6-18i:m4a-6-17i:m4a-6-17i:m4a-6-17i:m4a-6-17i:m4a-6-16i:m4a-6-16i:m4a-6-16i:m4a-6-16i:m4a-6-15i:m4a-6-15i:m4a-6-15i:m4a-6-15i:m4a-6-14i:m4a-6-14i:m4a-6-14i:m4a-6-14i:m4a-6-13i:m4a-6-13i:m4a-6-13i:m4a-6-13i:m4a-6-12i:m4a-6-12i:m4a-6-12i:m4a-6-12i:m4a-6-11i:m4a-6-11i:m4a-6-11i:m4a-6-11i:m4a-6-10i:m4a-6-10i:m4a-6-10i:m4a-6-10i:m4a-6-9i:m4a-6-9i:m4a-6-9i:m4a-6-9i:m4a-6-8i:m4a-6-8i:m4a-6-8i:m4a-6-8i:m4a-6-7i:m4a-6-7i:m4a-6-7i:m4a-6-7i:m4a-6-6i:m4a-6-6i:m4a-6-6i:m4a-6-6i:m4a-6-5i:m4a-6-5i:m4a-6-5i:m4a-6-5i:m4a-6-4i:m4a-6-4i:m4a-6-4i:m4a-6-4i:m4a-6-3i:m4a-6-3i:m4a-6-3i:m4a-6-3i:m4a-6-2i:m4a-6-2i:m4a-6-2i:m4a-6-2i:m4a-6-1i:m4a-6-1i:m4a-6-1i:m4a-6-1i:'
>>
>> MPIRUN_RANK=16 MPIRUN_NPROCS=128 MPIRUN_ID=32469
>> /ibrix/home/mfm42/opt/namd-IB/Linux-amd64-MPI/namd2 +strategy USE_GRID
>> equil3_sys.namd
>>
>> Any suggestions for that kind of error will be appreciated.
>>
>>
>> My system info:
>>
>> Dell 1855 Linux cluster consisting that is equipped with four Intel Xeon
>> EM64T processors (3.6GHz) and 8 GB of memory. The nodes are connected
>> with Infiniband, a high-speed, low-latency copper interconnect.
>>
>>
>>
>> --
>>
>>
>>
>> /*Morad Alawneh*/
>>
>> *Department of Chemistry and Biochemistry*
>>
>> *C100 BNSN, BYU*
>>
>> *Provo, UT 84602*
>>
>>

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