Re: build smp version of namd with intel 10.1

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Aug 08 2008 - 05:18:42 CDT

Dear Gengbin,

Thanks a lot! I managed to build the net-linux-amd64-smp version with
intel compilers 10.1 using -O1 instead of -O3. The megatest run as ./pgm
+p2 completed correctly. Now I tried to build the
mpi-linux-amd64-pthreads-smp version, I managed to build it correctly
but the megatest fails with the error message below both when run as
"./pgm +p2" or "mpirun -n1 -machinefile machines pgm +p2" (the file
machines contains one line with the machine name).

Now I have 2 questions, Is the pthreads option required when building an
smp version for mpi charm ? What is actually the difference between
building the mpi-linux-amd64-smp with and without pthreads option?
And the last question: Does anyone know why I get the error message below?

Thanks a lot for all the help

Best wishes
vlad

------------error-----------------------------------------------------------

Megatest is running on 1 nodes 1 processors.
test 0: initiated [callback (olawlor)]
[node-06-01:30629] *** Process received signal ***
[node-06-01:30629] Signal: Segmentation fault (11)
[node-06-01:30629] Signal code: Address not mapped (1)
[node-06-01:30629] Failing at address: 0x10
[node-06-01:30629] [ 0] /lib/libpthread.so.0 [0x2b19ad1ed410]
[node-06-01:30629] [ 1] /lib/libpthread.so.0(__pthread_mutex_lock+0x10)
[0x2b19ad1e8c60]
[node-06-01:30629] [ 2] pgm [0x4d49e6]
[node-06-01:30629] [ 3] /lib/libpthread.so.0 [0x2b19ad1e6f1a]
[node-06-01:30629] [ 4] /lib/libc.so.6(__clone+0x72) [0x2b19ae4a15d2]
[node-06-01:30629] *** End of error message ***
mpirun noticed that job rank 0 with PID 30629 on node node-06-01 exited
on signal 11 (Segmentation fault).

Gengbin Zheng wrote:
>
> That file just crashes the intel compiler. Try turn off -O3 on that
> particular file.
>
> Gengbin
>
> Vlad Cojocaru wrote:
>> Dear NAMD users,
>>
>> Does anyone have any experience on how to build an smp version of
>> namd with the intel 10.1 compilers for linux-amd64 architecture. I
>> would like to test if it brings anything in speed comparing to the
>> net tcp version I already compiled on our new cluster.
>> The bottleneck is the charm build so I also asked the charm
>> developers but I believe that if anybody on the namd list has
>> experience with this, I will get an answer much quicker.
>>
>> I managed to build the net-linux-amd64-smp version of charm++ with
>> gcc 4.1.2 correctly but when I tried with intel 10.1 I get the error
>> below (the error is the same for the mpi or net versions so don't get
>> disturbed by the mpicc line in the error message - happens the same
>> if it was icc).
>>
>> The problem with the gcc compilation is that the namd executable is
>> about 30 % slower than any of the intel compilations !
>>
>> Best wishes
>> vlad
>>
>> -----error with intel 10.1 when building
>> charm++---------------------------
>> ./bin/charmc -DCMK_OPTIMIZE=1 -O3 -fPIC -c -I. msgmgr.c
>> msgmgr.c(91): (col. 18) remark: LOOP WAS VECTORIZED.
>> ./bin/charmc -DCMK_OPTIMIZE=1 -O3 -fPIC -c -I. cpm.c
>> ./bin/charmc -DCMK_OPTIMIZE=1 -O3 -fPIC -c -I. cpthreads.c
>> ./bin/charmc -DCMK_OPTIMIZE=1 -O3 -fPIC -c -I. futures.c
>> ./bin/charmc -DCMK_OPTIMIZE=1 -O3 -fPIC -c -I. cldb.c
>> ./bin/charmc -DCMK_OPTIMIZE=1 -O3 -fPIC -c -I. topology.C
>> ./bin/charmc -DCMK_OPTIMIZE=1 -O3 -fPIC -c -I. random.c
>> ./bin/charmc -DCMK_OPTIMIZE=1 -O3 -fPIC -c -I. debug-conv.c
>> (0): internal error: 0_1561
>>
>> compilation aborted for debug-conv.c (code 4)
>> Fatal Error by charmc in directory
>> /home/cojocaru/apps/intel/charm/charm-cvs-mpi-smp-pthreads/mpi-linux-amd64-pthreads-smp-mpicxx/tmp
>>
>> Command mpicc -D_REENTRANT -I../bin/../include -D__CHARMC__=1
>> -DCMK_OPTIMIZE=1 -I. -O3 -fPIC
>> -I/apps/mpi/mvapich/1.0.1-2533-intel-10.1/include -c debug-conv.c -o
>> debug-conv.o returned error code 4
>> charmc exiting...
>> gmake[2]: *** [debug-conv.o] Error 1
>> gmake[2]: Leaving directory
>> `/home/cojocaru/apps/intel/charm/charm-cvs-mpi-smp-pthreads/mpi-linux-amd64-pthreads-smp-mpicxx/tmp'
>>
>> gmake[1]: *** [converse] Error 2
>> gmake[1]: Leaving directory
>> `/home/cojocaru/apps/intel/charm/charm-cvs-mpi-smp-pthreads/mpi-linux-amd64-pthreads-smp-mpicxx/tmp'
>>
>> gmake: *** [charm++] Error 2
>> -------------------------------------------------
>> Charm++ NOT BUILT. Either cd into
>> mpi-linux-amd64-pthreads-smp-mpicxx/tmp and try
>> to resolve the problems yourself, visit
>> http://charm.cs.uiuc.edu/
>> for more information. Otherwise, email the developers at ppl_at_cs.uiuc.edu
>> --
>> ----------------------------------------------------------------------------
>>
>> Dr. Vlad Cojocaru
>>
>> EML Research gGmbH
>> Schloss-Wolfsbrunnenweg 33
>> 69118 Heidelberg
>>
>> Tel: ++49-6221-533266
>> Fax: ++49-6221-533298
>>
>> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>>
>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>> ----------------------------------------------------------------------------
>>
>> EML Research gGmbH
>> Amtgericht Mannheim / HRB 337446
>> Managing Partner: Dr. h.c. Klaus Tschira
>> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
>> http://www.eml-r.org
>> ----------------------------------------------------------------------------
>>
>>
>>
>
>

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
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