[mvapich-discuss] compile charm++ and namd with mvapich
1.0.1and/or mvapich2
Vlad Cojocaru
Vlad.Cojocaru at eml-r.villa-bosch.de
Fri Aug 15 08:42:18 EDT 2008
Dear Dhabaleswar, Dear Mehdi,
Thanks a lot for your answers. I do have the user guide in front of my
eyes but I still cannot explain all the references to
/home/7/curtisbr/svn/mvapich2/mvapich2-1.2rc1 in the Makefile.in files
in the source tree ....
It looks as if after replacing those with ${master_top_srcdir} mvapich2
builds correctly .. I still have to test it though ...
Is the gfortran stuff relevant since I do not use gfortran ?
Cheers
vlad
Dhabaleswar Panda wrote:
> Vald,
>
> Please take a look at the detailed user guides of MVAPICH and MVAPICH2
> regarding how to build and install these packages. They are available from
> the following URL:
>
> http://mvapich.cse.ohio-state.edu/support/
>
> MVAPICH2 1.2 series has full autoconf-based configuration framework. It
> should significantly help you.
>
> DK
>
>
> On Fri, 15 Aug 2008, Vlad Cojocaru wrote:
>
>
>> Thanks Mehdi for all details,
>>
>> I guess you mean gcc when you say gfortran ... namd is not written in
>> fortran but in charm++ which is an adaptation of c++...
>>
>> Well, we have debian here so we used Debian packages to install the
>> inifiniband libs and headers ...(our sys administrator did that). Then I
>> tried to compile mvapich 1.0.1 and I found that I need the drastically
>> change the make.mvapich.gen2 file in order to get it to build (since the
>> defaults for $IBHOME are very strange ... we have everything in
>> /usr/include/infiniband and /usr/lib/infiniband ). After all I managed
>> to get it built but the namd hangs ....
>>
>> So I decided to try mvapich2 (1.2rc1 version) and I found lots problems.
>> Some of them I could fix but some are very strange. For instance in the
>> entire source tree there are lots of references to strange directories
>> /home/daffy ... or /home/7 ... and so on .. Some of them I replaced with
>> ${master_top_srcdir} since I figured out that one should replace them
>> but others I don't know ... Also, when I tried to build with shared
>> libs, the make is not able to build the mpiname application ... I could
>> not figure out why ...
>>
>> So, lots of problems ....I'll try to figure them out ... However, the
>> problems with mvapich2 look more as bugs in the Makefiiles .. So, maybe
>> somebody would like to change those ...
>>
>> Cheers
>> vlad
>>
>>
>> Mehdi Bozzo-Rey wrote:
>>
>>> Hi Vlad,
>>>
>>>
>>>
>>> No, I did not use the intel compilers (not yet). I used gfortran. More
>>> precisely:
>>>
>>>
>>>
>>> OS:
>>>
>>>
>>>
>>> RHEL 5.1 (Kernel 2.6.18-53.el5)
>>>
>>>
>>>
>>> [mbozzore at tyan04 ~]$ mpicc --version
>>>
>>> gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
>>>
>>>
>>>
>>> [mbozzore at tyan04 ~]$ mpicxx --version
>>>
>>> g++ (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
>>>
>>>
>>>
>>> [mbozzore at tyan04 ~]$ mpif77 --version
>>>
>>> GNU Fortran (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
>>>
>>>
>>>
>>> [mbozzore at tyan04 ~]$ mpif90 --version
>>>
>>> GNU Fortran (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
>>>
>>>
>>>
>>> Hardware: intel quads for the nodes, topspin switch and hcas for IB.
>>>
>>>
>>>
>>>
>>>
>>> Yes, I used OFED (1.3).
>>>
>>>
>>>
>>> I did not enable sharedlibs for that build.
>>>
>>>
>>>
>>> I will double check but if I remember well, everything was fine
>>> (compilation) on the mvapich2 side. What version did you use ?
>>>
>>>
>>>
>>> Cheers,
>>>
>>>
>>>
>>> Mehdi
>>>
>>>
>>>
>>> Mehdi Bozzo-Rey
>>> Open Source Solution Developer
>>> Platform computing
>>> Phone : +1 905 948 4649
>>> E-mail : mbozzore at platform.com <mailto:mbozzore at platform.com>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *From:* Cojocaru,Vlad [mailto:vlad.cojocaru at eml-r.villa-bosch.de]
>>> *Sent:* August-14-08 4:35 PM
>>> *To:* Mehdi Bozzo-Rey; mvapich-discuss at cse.ohio-state.edu
>>> *Subject:* RE: [mvapich-discuss] compile charm++ and namd with mvapich
>>> 1.0.1and/or mvapich2
>>>
>>>
>>>
>>> Hi Mehdi,
>>>
>>> Did you use intel 10.1 as well ? Did you build on openfabrics ? what
>>> compiler flags did you pass to the mvapich build? Did you build with
>>> --enable sharedlib or without? I would be grateful If you give me some
>>> bits of the details how you built mvapich?.
>>> Thanks for the reply. Yes, there is something about the compilation of
>>> mvapich. As I said I successfully compiled NAMD on a cluster that had
>>> already mvapich compiled with intel as the default mpi lib. However,
>>> on the new cluster (quad cores AMD opterons with mellanox infiniband)
>>> I got these problems. So, its definitely the mvapich build which
>>> fails although I don't get any errors fro make.
>>>
>>> Any idea why the mpiname application fails to compile when compiling
>>> mvapich2 ?
>>>
>>> Thanks again
>>>
>>> Best wishes
>>> vlad
>>>
>>>
>>> -----Original Message-----
>>> From: Mehdi Bozzo-Rey [mailto:mbozzore at platform.com]
>>> Sent: Thu 8/14/2008 7:20 PM
>>> To: Cojocaru,Vlad; mvapich-discuss at cse.ohio-state.edu
>>> Subject: RE: [mvapich-discuss] compile charm++ and namd with mvapich
>>> 1.0.1and/or mvapich2
>>>
>>> Hello Vlad,
>>>
>>>
>>> I just recompiled NAMD and it looks ok for me (output of simple test
>>> below). I guess the problem is on the compilation side.
>>>
>>> Best regards,
>>>
>>> Mehdi
>>>
>>> Mehdi Bozzo-Rey
>>> Open Source Solution Developer
>>> Platform computing
>>> Phone : +1 905 948 4649
>>> E-mail : mbozzore at platform.com
>>>
>>>
>>> [mbozzore at tyan04 Linux-amd64-MPI]$ mpirun_rsh -np 8 -hostfile
>>> ./hosts.8 ./namd2 src/alanin
>>> Charm++> Running on MPI version: 1.2 multi-thread support: 1/1
>>> Charm warning> Randomization of stack pointer is turned on in Kernel,
>>> run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable
>>> it. Thread migration may not work!
>>> Info: NAMD 2.6 for Linux-amd64-MPI
>>> Info:
>>> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
>>> Info: and send feedback or bug reports to namd at ks.uiuc.edu
>>> Info:
>>> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
>>> Info: in all publications reporting results obtained with NAMD.
>>> Info:
>>> Info: Based on Charm++/Converse 50914 for
>>> mpi-linux-x86_64-gfortran-smp-mpicxx
>>> Info: Built Thu Aug 14 13:12:02 EDT 2008 by mbozzore on
>>> tyan04.lsf.platform.com
>>> Info: 1 NAMD 2.6 Linux-amd64-MPI 8 compute-00-00.ocs5.org mbozzore
>>> Info: Running on 8 processors.
>>> Info: 8208 kB of memory in use.
>>> Info: Memory usage based on mallinfo
>>> Info: Changed directory to src
>>> Info: Configuration file is alanin
>>> TCL: Suspending until startup complete.
>>> Info: SIMULATION PARAMETERS:
>>> Info: TIMESTEP 0.5
>>> Info: NUMBER OF STEPS 9
>>> Info: STEPS PER CYCLE 3
>>> Info: LOAD BALANCE STRATEGY Other
>>> Info: LDB PERIOD 600 steps
>>> Info: FIRST LDB TIMESTEP 15
>>> Info: LDB BACKGROUND SCALING 1
>>> Info: HOM BACKGROUND SCALING 1
>>> Info: MAX SELF PARTITIONS 50
>>> Info: MAX PAIR PARTITIONS 20
>>> Info: SELF PARTITION ATOMS 125
>>> Info: PAIR PARTITION ATOMS 200
>>> Info: PAIR2 PARTITION ATOMS 400
>>> Info: MIN ATOMS PER PATCH 100
>>> Info: INITIAL TEMPERATURE 0
>>> Info: CENTER OF MASS MOVING INITIALLY? NO
>>> Info: DIELECTRIC 1
>>> Info: EXCLUDE SCALED ONE-FOUR
>>> Info: 1-4 SCALE FACTOR 0.4
>>> Info: NO DCD TRAJECTORY OUTPUT
>>> Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
>>> Info: NO VELOCITY DCD OUTPUT
>>> Info: OUTPUT FILENAME output
>>> Info: BINARY OUTPUT FILES WILL BE USED
>>> Info: NO RESTART FILE
>>> Info: SWITCHING ACTIVE
>>> Info: SWITCHING ON 7
>>> Info: SWITCHING OFF 8
>>> Info: PAIRLIST DISTANCE 9
>>> Info: PAIRLIST SHRINK RATE 0.01
>>> Info: PAIRLIST GROW RATE 0.01
>>> Info: PAIRLIST TRIGGER 0.3
>>> Info: PAIRLISTS PER CYCLE 2
>>> Info: PAIRLISTS ENABLED
>>> Info: MARGIN 1
>>> Info: HYDROGEN GROUP CUTOFF 2.5
>>> Info: PATCH DIMENSION 12.5
>>> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
>>> Info: TIMING OUTPUT STEPS 15
>>> Info: USING VERLET I (r-RESPA) MTS SCHEME.
>>> Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
>>> Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
>>> Info: RANDOM NUMBER SEED 1218734148
>>> Info: USE HYDROGEN BONDS? NO
>>> Info: COORDINATE PDB alanin.pdb
>>> Info: STRUCTURE FILE alanin.psf
>>> Info: PARAMETER file: XPLOR format! (default)
>>> Info: PARAMETERS alanin.params
>>> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
>>> Info: SUMMARY OF PARAMETERS:
>>> Info: 61 BONDS
>>> Info: 179 ANGLES
>>> Info: 38 DIHEDRAL
>>> Info: 42 IMPROPER
>>> Info: 0 CROSSTERM
>>> Info: 21 VDW
>>> Info: 0 VDW_PAIRS
>>> Info: ****************************
>>> Info: STRUCTURE SUMMARY:
>>> Info: 66 ATOMS
>>> Info: 65 BONDS
>>> Info: 96 ANGLES
>>> Info: 31 DIHEDRALS
>>> Info: 32 IMPROPERS
>>> Info: 0 CROSSTERMS
>>> Info: 0 EXCLUSIONS
>>> Info: 195 DEGREES OF FREEDOM
>>> Info: 55 HYDROGEN GROUPS
>>> Info: TOTAL MASS = 783.886 amu
>>> Info: TOTAL CHARGE = 8.19564e-08 e
>>> Info: *****************************
>>> Info: Entering startup phase 0 with 8208 kB of memory in use.
>>> Info: Entering startup phase 1 with 8208 kB of memory in use.
>>> Info: Entering startup phase 2 with 8208 kB of memory in use.
>>> Info: Entering startup phase 3 with 8208 kB of memory in use.
>>> Info: PATCH GRID IS 1 BY 1 BY 1
>>> Info: REMOVING COM VELOCITY 0 0 0
>>> Info: LARGEST PATCH (0) HAS 66 ATOMS
>>> Info: CREATING 11 COMPUTE OBJECTS
>>> Info: Entering startup phase 4 with 8208 kB of memory in use.
>>> Info: Entering startup phase 5 with 8208 kB of memory in use.
>>> Info: Entering startup phase 6 with 8208 kB of memory in use.
>>> Measuring processor speeds... Done.
>>> Info: Entering startup phase 7 with 8208 kB of memory in use.
>>> Info: CREATING 11 COMPUTE OBJECTS
>>> Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
>>> Info: NONBONDED TABLE SIZE: 705 POINTS
>>> Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 3.38813e-21 AT 7.99609
>>> Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.27241e-16 AT 7.99609
>>> Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 6.77626e-21 AT 7.99609
>>> Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.1972e-16 AT 7.99609
>>> Info: Entering startup phase 8 with 8208 kB of memory in use.
>>> Info: Finished startup with 8208 kB of memory in use.
>>> ETITLE: TS BOND ANGLE DIHED
>>> IMPRP ELECT VDW BOUNDARY
>>> MISC KINETIC TOTAL TEMP
>>> TOTAL2 TOTAL3 TEMPAVG
>>>
>>> ENERGY: 0 0.0050 0.4192 0.0368
>>> 0.4591 -210.1610 1.0506 0.0000
>>> 0.0000 0.0000 -208.1904 0.0000
>>> -208.1877 -208.1877 0.0000
>>>
>>> ENERGY: 1 0.0051 0.4196 0.0367
>>> 0.4585 -210.1611 1.0184 0.0000
>>> 0.0000 0.0325 -208.1905 0.1675
>>> -208.1878 -208.1877 0.1675
>>>
>>> ENERGY: 2 0.0058 0.4208 0.0365
>>> 0.4568 -210.1610 0.9219 0.0000
>>> 0.0000 0.1285 -208.1907 0.6632
>>> -208.1881 -208.1877 0.6632
>>>
>>> ENERGY: 3 0.0092 0.4232 0.0361
>>> 0.4542 -210.1599 0.7617 0.0000
>>> 0.0000 0.2845 -208.1910 1.4683
>>> -208.1885 -208.1878 1.4683
>>>
>>> ENERGY: 4 0.0176 0.4269 0.0356
>>> 0.4511 -210.1565 0.5386 0.0000
>>> 0.0000 0.4952 -208.1914 2.5561
>>> -208.1890 -208.1878 2.5561
>>>
>>> ENERGY: 5 0.0327 0.4327 0.0350
>>> 0.4480 -210.1489 0.2537 0.0000
>>> 0.0000 0.7552 -208.1917 3.8977
>>> -208.1894 -208.1879 3.8977
>>>
>>> ENERGY: 6 0.0552 0.4409 0.0343
>>> 0.4454 -210.1354 -0.0915 0.0000
>>> 0.0000 1.0592 -208.1920 5.4666
>>> -208.1898 -208.1880 5.4666
>>>
>>> ENERGY: 7 0.0839 0.4522 0.0334
>>> 0.4440 -210.1137 -0.4951 0.0000
>>> 0.0000 1.4031 -208.1922 7.2418
>>> -208.1900 -208.1882 7.2418
>>>
>>> ENERGY: 8 0.1162 0.4674 0.0325
>>> 0.4448 -210.0822 -0.9550 0.0000
>>> 0.0000 1.7839 -208.1923 9.2074
>>> -208.1902 -208.1883 9.2074
>>>
>>> ENERGY: 9 0.1492 0.4870 0.0315
>>> 0.4485 -210.0391 -1.4687 0.0000
>>> 0.0000 2.1990 -208.1925 11.3497
>>> -208.1905 -208.1884 11.3497
>>>
>>> WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 9
>>> WRITING COORDINATES TO OUTPUT FILE AT STEP 9
>>> WRITING VELOCITIES TO OUTPUT FILE AT STEP 9
>>> ==========================================
>>> WallClock: 4.172574 CPUTime: 4.167367 Memory: 8208 kB
>>> End of program
>>>
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: mvapich-discuss-bounces at cse.ohio-state.edu
>>> [mailto:mvapich-discuss-bounces at cse.ohio-state.edu] On Behalf Of Vlad
>>> Cojocaru
>>> Sent: August-14-08 11:32 AM
>>> To: mvapich-discuss at cse.ohio-state.edu
>>> Subject: [mvapich-discuss] compile charm++ and namd with mvapich
>>> 1.0.1and/or mvapich2
>>>
>>> Dear mvapich users,
>>>
>>> I tried to compile mvapich1.0.1, charm++ and namd on our new Linux-amd64
>>> infiniband cluster using the intel 10.1.015 compilers. With
>>> mvapich1.0.1, I managed to build mvapich1.0.1, tested the programs in
>>> the /examples directory. Then, I bult charm++ and tested it with
>>> "mpirun_rsh -n 2" .. All tests passed correctly. Then I built namd on
>>> top of mvapich1.0.1 and charm,
>>>
>>> Everything seemed ok only that the namd executable hangs without error
>>> messages. In fact it appears as if it still runs but it doesn't produce
>>> any output. If I repeat exactly the same procedure but with openmpi
>>> instead of mvapich, everything works fine ....(however I am not so happy
>>> about the scaling of openmpi on infiniband)
>>>
>>> Does anyone have experience with installing namd using mvapich1.0.1 ? If
>>> yes, any idea why this happens? I must say when I did the same on
>>> another cluster which had mvapich1.0.1 already compiled with the intel
>>> compilers, everything worked out correcltly. So, it must be something
>>> with the compilation of mvapich1.0.1 on our new infiniband setup that
>>> creates the problem.
>>>
>>> The german in the error simply says that executable "mpiname was not
>>> found"
>>>
>>> Best wishes
>>> vlad
>>>
>>> ----------------------------------error------------------------------------------------------------------------
>>> I also tried mvapich2 but the compilation fails when installing the
>>> mpiname application (see error below) which apparently fails to compile
>>> (no executable is found in /env/mpiname dir). However no error messages
>>> are printed by make and the build completes correctly. So I am not sure
>>> why mpiname does not compile and still make install tries to install
>>> it ...
>>>
>>> /usr/bin/install -c mpiname/mpiname
>>> /sw/mcm/app/vlad/mpi/C07/mvapich2/1.2/bin/mpiname
>>> /usr/bin/install: Aufruf von stat für ?mpiname/mpiname? nicht möglich:
>>> Datei oder Verzeichnis nicht gefunden
>>> make[1]: *** [install] Fehler 1
>>> make[1]: Leaving directory
>>> `/sw/mcm/app/vlad/mpi/C07/mvapich2/1.2-src/src/env'
>>> make: *** [install] Fehler 2
>>>
>>> --
>>> ----------------------------------------------------------------------------
>>> 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
>>> ----------------------------------------------------------------------------
>>>
>>>
>>> _______________________________________________
>>> mvapich-discuss mailing list
>>> mvapich-discuss at cse.ohio-state.edu
>>> http://mail.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss
>>>
>>>
>> --
>> ----------------------------------------------------------------------------
>> 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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