From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Thu Oct 14 2004 - 14:03:12 CDT
If it is intel compiler, try get the latest patch from intel. It should
help.
Gengbin
Alberto Santana wrote:
>Compiled with the -O0 option. Ran namd2 with the ++debug and it went very
>well, no problems nor warnings of any kind. My guess is that now I can start
>increasing the optimization level until it breaks.
>
>Alberto
>
>On Thursday 14 October 2004 02:20 pm, you wrote:
>
>
>>HI Alberto
>>
>>Ramp down the optimization for namd and add the ++debug switch when
>>running the namd test case. I have seen this error before but it was a
>>long time ago. It might have even been a input script problem when I saw
>>it. So just check the system size parameters for any extraneous
>>characters.
>>
>>Brian
>>
>>On Thu, 14 Oct 2004, Alberto Santana wrote:
>>
>>
>>>I followed Florian's suggestion and built charm++ with:
>>>
>>>build charm++ mpi-linux icc gm2 -O2 -L/usr/rels/mpich/lib/shared
>>>-I/usr/rels/mpich/include -L/usr/rels/mpich/lib
>>>-L/opt/gm/lib -I/opt/gm/include -lmpich -lgm -DCMK_OPTIMIZE=1
>>>
>>> and added -lpmpich and -lpthread before compiling namd2, otherwise it
>>>won't compile.
>>>
>>>The charm++ test goes well. When running the BPTI files used to do the
>>>benchmark it aborts with
>>>...
>>>Info: 2643 DEGREES OF FREEDOM
>>>Info: 449 HYDROGEN GROUPS
>>>Info: TOTAL MASS = 6446.48 amu
>>>Info: TOTAL CHARGE = 6 e
>>>Info: *****************************
>>>Info: Entering startup phase 0 with 43082 kB of memory in use.
>>>Info: Entering startup phase 1 with 43082 kB of memory in use.
>>>Info: Entering startup phase 2 with 43272 kB of memory in use.
>>>Info: Entering startup phase 3 with 43278 kB of memory in use.
>>>FATAL ERROR: Bug in PatchMap::initialize - negative grid dimension.
>>>FATAL ERROR: Bug in PatchMap::initialize - negative grid dimension.
>>>[0] MPI Abort by user Aborting program !
>>>[0] Aborting program!
>>>
>>>Note that I used -O2 as suggested by Gengbin
>>>(http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/0693.html)
>>>
>>>Alberto
>>>
>>>On Monday 11 October 2004 08:49 pm, you wrote:
>>>
>>>
>>>>Hello Alberto,
>>>>
>>>>i recently (two days ago) compiled NAMD 2.5 on my linux cluster with
>>>>myrinet. in order for charm to work with myrinet i compiled it with
>>>>
>>>>./build charm++ mpi-linux gm2 -O3 -I$MPICH/include -L$MPICH/lib
>>>>-L$GM/lib -lmpich -lgm -DCMK_OPTIMIZE=1
>>>>
>>>>note the gm2 flag for gm version 2.xx. as i have athlon cpus i didn't
>>>>use icc but gcc3.3 instead. you must have mpich-gm >1.2.5..12 installed
>>>>in oder for everything to work (at least with the mpi-linux version).
>>>>mpich-gm should be compiled with the same compiler used for building
>>>>charm.
>>>>
>>>>Regards
>>>>
>>>> Florian Barth
>>>>
>>>>
>>*****************************************************************
>>**Brian Bennion, Ph.D. **
>>**Computational and Systems Biology Division **
>>**Biology and Biotechnology Research Program **
>>**Lawrence Livermore National Laboratory **
>>**P.O. Box 808, L-448 bennion1_at_llnl.gov **
>>**7000 East Avenue phone: (925) 422-5722 **
>>**Livermore, CA 94550 fax: (925) 424-6605 **
>>*****************************************************************
>>
>>
>
>
>
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