Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI

From: Christopher Gillespie (gillescche_at_gmail.com)
Date: Wed Aug 27 2008 - 12:49:31 CDT

Hi Frank,

I am working through a similar problem on a Rocks cluster of ours.
Looking through the mailing lists I found the solution to your first
problem.

You need to change the relevant parts, including lmpich to lmpi, in
conv-mach.sh which is in charm/src/arch/mpi-linux. As for the second,
I haven't gotten that far.

Good Luck

Chris

On Aug 27, 2008, at 12:41 PM, Frank Thommen wrote:

> Hi,
>
> I'm currently trying to build NAMD 2.6 on a PBS cluster with "built-
> in" LAM/MPI.
>
> First of all: Do I understand correctly, that none the binary
> distributions of NAMD 2.6 (as listed on http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD)
> is built with MPI support (and possible for x86_64 architecture)?
>
> Then...
>
>
> First problem
> -------------
>
> The first problem appears with charm 5.9. After having built it
> with `./build charm++ mpi-linux-amd64 --no-shared -O -
> DCMK_OPTIMIZE=1` I cd to 'tests/charm++/megatest/' and do `make pgm`
> which finishes with the following error:
>
> # make pgm
> [... output shortened ...]
> ./../../bin/charmc -o bitvector.o bitvector.C
> ./../../bin/charmc -o pgm megatest.o groupring.o nodering.o
> varsizetest.o varraystest.o groupcast.o nodecast.o synctest.o fib.o
> arrayring.o tempotest.o packtest.o queens.o migration.o marshall.o
> priomsg.o priotest.o rotest.o statistics.o templates.o inherit.o
> reduction.o callback.o immediatering.o bitvector.o -language charm++
> /usr/bin/ld: cannot find -lmpich
> collect2: ld returned 1 exit status
> mpiCC: No such file or directory
> Fatal Error by charmc in directory /usr/struct/pack/namd2_mpi-2.0.6/
> SRC/NAMD_2.6_Source/charm-5.9/tests/charm++/megatest
> Command mpiCC -m64 -fPIC -rdynamic -o pgm -L../../../bin/../lib -
> I../../../bin/../include ../../../bin/../lib/libldb-rand.o
> megatest.o groupring.o nodering.o varsizetest.o varraystest.o
> groupcast.o nodecast.o synctest.o fib.o arrayring.o tempotest.o
> packtest.o queens.o migration.o marshall.o priomsg.o priotest.o
> rotest.o statistics.o templates.o inherit.o reduction.o callback.o
> immediatering.o bitvector.o moduleinit11129.o ../../../bin/../lib/
> libmemory-default.o ./../../bin/../lib/libthreads-default.o -lck -
> lconv-cplus-y -lconv-core -lconv-util -lckqt -lmpich -ldl -lmpich -
> lm returned error code 1
> charmc exiting...
> make: *** [pgm] Error 1
> #
>
> `libmpich` is in fact not there as this is LAM/MPI. The LAM/MPI
> libraries I can find are:
>
> /usr/lib64/liblam.a
> /usr/lib64/liblam.la
> /usr/lib64/liblamf77mpi.a
> /usr/lib64/liblamf77mpi.la
> /usr/lib64/liblammpi++.a
> /usr/lib64/liblammpi++.la
> /usr/lib64/liblammpio.a
> /usr/lib64/libmpi.a
> /usr/lib64/libmpi.la
>
> I would love to replace -lmpich by -lmpi but I didn't find where
> this option is defined.
>
>
>
> Second problem
> --------------
>
> I decided to ignore that and went on to build NAMD. Edited
> Make.charm, arch/Linux-amd64.fftw and arch/Linux-amd64.tcl, did `./
> config tcl fftw Linux-amd64-MPI` and `make` in Linux-amd64-MPI,
> which results in the following errors:
>
> # make
> [... output shortened...]
> [xsoft_at_clnode154 Linux-amd64-MPI]$ make
> g++ -I/usr/struct/pack/namd2_mpi-2.0.6/SRC/NAMD_2.6_Source/charm-5.9/
> mpi-linux-amd64/include -DCMK_OPTIMIZE=1 -Isrc -Iinc -Iplugins/
> include -I/usr/include -I/home/xsoft/tcl/include -DNAMD_TCL -I/usr/
> struct/pack/fftw-3.1.2/include -I/home/xsoft/fftw/include -
> DNAMD_FFTW -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI
> \" -O3 -m64 -fexpensive-optimizations -ffast-math -o obj/
> ComputePme.o -c src/ComputePme.C
> src/ComputePme.C:12:19: sfftw.h: No such file or directory
> src/ComputePme.C:13:20: srfftw.h: No such file or directory
> [...removed lots and lots of collateral errors...]
> #
>
> In fact /usr/struct/pack/fftw-3.1.2/include contains only fftw3.f
> and fftw3.h and /usr/struct/pack/fftw-3.1.2/lib64 contains:
>
> # ls /usr/struct/pack/fftw-3.1.2/lib64
> libfftw3.a libfftw3f.so libfftw3.la libfftw3.so.3.1.2
> libfftw3f.a libfftw3f.so.3 libfftw3.so pkgconfig
> libfftw3f.la libfftw3f.so.3.1.2 libfftw3.so.3
> #
>
>
> No sfftw* or libsfftw* whatsover. This is a fresh FFTW-build from
> source.
>
>
> Any ideas or thoughts how to solve or work around any of the two
> problems? All hints are welcome.
>
>
> Thanks
>
> frank
>
> --
> Frank Thommen - Structures IT Management and Support - EMBL Heidelberg
> frank.thommen_at_embl-heidelberg.de - +49 6221 387 8353
>

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