[mvapich-discuss] compile charm++ and namd with mvapich
1.0.1and/or mvapich2
Dhabaleswar Panda
panda at cse.ohio-state.edu
Fri Aug 15 08:32:59 EDT 2008
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 âmpiname/mpinameâ 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
> ----------------------------------------------------------------------------
>
>
>
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