[mvapich-discuss] compile charm++ and namd with mvapich
1.0.1and/or mvapich2
Jonathan Perkins
perkinjo at cse.ohio-state.edu
Fri Aug 15 09:18:14 EDT 2008
Vlad:
Can you please send us your config.log and make.log files. Those
references to /home/7/curtisbr should only be present to create the
Makefile.in files that are already present in the tarball. Also, I do
not know why mpiname is failing to build for you but it should not
affect the functionality of any mpi programs.
On Fri, Aug 15, 2008 at 02:42:18PM +0200, Vlad Cojocaru wrote:
> 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
> ----------------------------------------------------------------------------
>
>
> _______________________________________________
> mvapich-discuss mailing list
> mvapich-discuss at cse.ohio-state.edu
> http://mail.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss
--
Jonathan Perkins
http://www.cse.ohio-state.edu/~perkinjo
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