Re: Problems compiling NAMD

From: Alexander A. Vakhrushev (makaveli.lcf_at_gmail.com)
Date: Tue Oct 07 2008 - 05:04:47 CDT

Hi Jesper,

yes that is good approach to start from simple configuration to complicated one.

2008/10/7 Jesper Soerensen <jes_at_chem.au.dk>:
> Hi Alexander,
>
> I'm assuming that if I don't specify a compiler it defaults to gcc?
> Then yes I have made a version of gcc without MPI, but once I add MPI it
> fails. It seems to be that our MPI has been compiled with either intel
> or pgi compilers and so gcc fails because MPI calls some intel keywords.
>
> for example while running Make pgm:
>
>>/com/mpich-1.2.7p1/lib/libmpich.a(dmpipk.o)(.text+0x249): In function
>>`MPIR_UnPack_Hvector':
>>: undefined reference to `_intel_fast_memcpy'
>
> I can ask our sysadmin to make a gcc version of MPI and see if that
> helps. Would that be a good idea?
>
> Kind regards,
> Jesper
>
>
>
> On Mon, 2008-10-06 at 21:00 +0500, Alexander A. Vakhrushev wrote:
>> Hi Jesper!
>>
>> Did you try just gcc version?
>>
>> 2008/10/6 Jesper Soerensen <jes_at_chem.au.dk>:
>> > Hi Alexander,
>> >
>> > I'm running CentOS 4.3. I've tried using both OpenMPI and MPICH but both
>> > fail. I've tried:
>> > OpenMPI version 1.2.6
>> > MPICH version 1.2.7
>> > Using Intel compilers (icc & ifort) version 10.1.017
>> >
>> > I ran the megatest set from charm++ and I get a failure in test14:
>> >
>> >> ./mpirun ./pgm
>> >> ...
>> >> test 14: initiated [tempotest (fang)]
>> >> p0_29927: p4_error: interrupt SIGSEGV: 11
>> >
>> >
>> >> mpirun -np 4 -all-local ./pgm
>> >> Megatest is running on 4 processors.
>> >> ...
>> >> test 14: initiated [tempotest (fang)]
>> >> p2_30323: p4_error: interrupt SIGSEGV: 11
>> >> p3_30346: p4_error: Found a dead connection while looking for
>> > messages: 0
>> >> [jesper_at_fe1 megatest]$ p1_30297: p4_error: interrupt SIGx: 13
>> >> rm_l_2_30324: (10.011719) net_send: could not write to fd=5, errno =
>> > 32
>> >> rm_l_3_30347: (7.667969) net_send: could not write to fd=5, errno = 32
>> >> p2_30323: (12.027344) net_send: could not write to fd=5, errno = 32
>> >> p3_30346: (13.675781) net_send: could not write to fd=5, errno = 32
>> >> p1_30297: (18.843750) net_send: could not write to fd=5, errno = 32
>> >
>> > Does anybody recognize this?
>> >
>> > Kind regards,
>> >
>> > Jesper
>> >
>> >
>> >
>> >
>> > On Fri, 2008-10-03 at 22:44 +0500, Alexander A. Vakhrushev wrote:
>> >> Hi Jesper!
>> >>
>> >> What is platform of your cluster?
>> >>
>> >> 2008/10/3 Jesper Soerensen <jes_at_chem.au.dk>:
>> >> > Hi,
>> >> >
>> >> > I've just compiled NAMD on our cluster and this runs through fine, but
>> >> > when I start a job I get the following error in the log file:
>> >> >>Info: Entering startup phase 8 with 134856 kB of memory in use.
>> >> >>Info: Finished startup with 143120 kB of memory in use.
>> >> >>1 additional process aborted (not shown)
>> >> >
>> >> > And the cluster job-error log says:
>> >> >>mpirun noticed that job rank 0 with PID 25232 on node s07n06 exited on
>> >> >>signal 11 (Segmentation fault).
>> >> >
>> >> > I am running a Linux-amd64-MPI-icc-ifort version if this helps. Also, let
>> >> > me know if there is more information I can give to help solve the
>> >> > problem. I'm just wondering if anybody has seen this type of error
>> >> > before.
>> >> >
>> >> > Kind regards,
>> >> >
>> >> > Jesper Soerensen
>> >> >
>> >> >
>> >> > --
>> >> > Jesper Srensen, M.Sc.
>> >> > Ph.D.-student
>> >> > Biomodelling Group, inSPIN and iNANO centers
>> >> > Department of Chemistry
>> >> > University of Aarhus
>> >> > Langelandsgade 140
>> >> > 8000 Aarhus C
>> >> > Office: 1510-419
>> >> > Tlf. 89423385
>> >> > email: jes_at_chem.au.dk
>> >> > www: www.chem.au.dk/~biomodelling
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >
>> >
>>
>>
>>
>
>

-- 
Best regards,
Dr. Alexander Vakhrushev
Institute of Applied Mechanics
Dep. of Mech. and Phys.-Chem.
of heterogeneous media
UB of Russian Academy of Sciences
34 T. Baramzinoy St.
Izhevsk, Russia 426067
----------------------------------
 ӬѬج֬߬ڬ֬,
    Ѭ֬ ݬ֬ܬѬ߬լ ݬ֬ܬѬ߬լӬڬ
..-.., ...
߬ڬ ڬܬݬѬլ߬ ެ֬Ѭ߬ڬܬ
ѬݬܬԬ լ֬ݬ֬߬ڬ
ڬ۬ܬ ܬѬլ֬ެڬ Ѭ
426067, . ج֬Ӭ
. . ѬѬެ٬ڬ߬ 34
+7(3412)21-45-83

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:56 CST