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Re: [charm] [ppl] make pgm error


Chronological Thread 
  • From: "Jain, Nikhil" <nikhil AT illinois.edu>
  • To: Dimar Jaime González Soto <dimar.gonzalez.soto AT gmail.com>
  • Cc: "charm AT cs.illinois.edu" <charm AT cs.illinois.edu>
  • Subject: Re: [charm] [ppl] make pgm error
  • Date: Tue, 19 Mar 2013 18:34:45 +0000
  • Accept-language: en-US
  • List-archive: <http://lists.cs.uiuc.edu/pipermail/charm/>
  • List-id: CHARM parallel programming system <charm.cs.uiuc.edu>

If you have successfully compiled NAMD, namd2 should be in /home/hpcadmin/software/NAMD_2.9_Source/Linux-x86_64-g++.

--Nikhil

--
Nikhil Jain, nikhil AT illinois.edu, http://charm.cs.uiuc.edu/people/nikhil
Doctoral Candidate @ CS, UIUC
 


From: Dimar Jaime González Soto <dimar.gonzalez.soto AT gmail.com>
Date: Tuesday, March 19, 2013 1:19 PM
To: "Zheng, Gengbin" <gzheng AT illinois.edu>
Cc: Nikhil Jain <nikhil AT illinois.edu>, "charm AT cs.illinois.edu" <charm AT cs.illinois.edu>
Subject: Re: [ppl] [charm] make pgm error
Resent-From: Nikhil Jain <nikhil AT illinois.edu>
Resent-Date: Tue, 19 Mar 2013 13:19:18 -0500

yes . I'm  not able to locate namd2.

Thanks for the information.

2013/3/19 Gengbin Zheng <gzheng AT illinois.edu>

building charm++ with mpi-linux-x86_64 assumes  mpicc and mpicxx mpi wrappers.
However, you can use MPICXX and MPICC environment variable to override them.

e.g (assuming bash):

MPICXX=hpCC  MPICC=hpcc   ./build charm++ mpi-linux-x86_64


Gengbin


On Tue, Mar 19, 2013 at 11:55 AM, Jain, Nikhil <nikhil AT illinois.edu> wrote:
Sorry, I failed to understand your trouble. You were not able to locate namd2?

As for using HP-MPI, even though they do not have a mpicxx wrapper, it is possible to install using them. One simple trick that can be done is to alias the mpic* wrappers to refer to HP-MPI compilers: something like 

alias mpicxx=hpCC

in you .bashrc (assuming hpCC is the name of HP's MPI compiler). If this does not work, I can change a few configuration files, and help you build it.

--Nikhil

--
Doctoral Candidate @ CS, UIUC
 


From: Dimar Jaime González Soto <dimar.gonzalez.soto AT gmail.com>
Date: Tuesday, March 19, 2013 9:22 AM
To: Nikhil Jain <nikhil AT illinois.edu>

Subject: Re: [charm] make pgm error
Resent-From: Nikhil Jain <nikhil AT illinois.edu>
Resent-Date: Tue, 19 Mar 2013 09:22:11 -0500

It worked!! thank you very much Jain.  I have another issue running this example:

Longer test using four processes: wget http://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz tar xzf apoa1.tar.gz ./charmrun ++local +p4 ./namd2 apoa1/apoa1.namd (FFT optimization will take a several seconds during the first run.)


I don't know where is the namd2 executable, I put the apoa1 directore in the root NAMD_2.9_Source  directory.

I chose the openmpi over the HP-MPI, because the hp-mpi doesn't have the mpicxx compiler(only the mpicc compiler) and it made the installation imposible.


2013/3/18 Jain, Nikhil <nikhil AT illinois.edu>

Ah, my bad, I dint notice the hp* missing calls. It appears to me that a mix up between openMPI and HP-MPI is causing the trouble. Given that compilation was done with openMPI, it should not be requesting function calls found in HP-MPI. One possible reason can be inclusion of mpi.h from HP-MPI during Charm compilation. Possible things to try-

1. Check you PATH environment variable, and confirm that openMPI is included before HP-MPI.
2. Try passing --basedir=/shared/openmpi-1.6.4 to build command for Charm: this will include -I/shared/openmpi-1.6.4/include and -L/shared/openmpi-1.6.4/lib during compilation of Charm.

--Nikhil

--
Doctoral Candidate @ CS, UIUC
 


From: Dimar Jaime González Soto <dimar.gonzalez.soto AT gmail.com>
Date: Monday, March 18, 2013 7:07 PM
To: Nikhil Jain <nikhil AT illinois.edu>
Cc: "charm AT cs.illinois.edu" <charm AT cs.illinois.edu>

Subject: Re: [charm] make pgm error
Resent-From: Nikhil Jain <nikhil AT illinois.edu>
Resent-Date: Mon, 18 Mar 2013 19:07:42 -0500

The LD_LIBRARY_PATH environment variable is properly configured in the .bashrc file:

LD_LIBRARY_PATH=/shared/openmpi-1.6.4/lib:/opt/platform_mpi/lib/linux_amd64:$LD_LIBRARY_PATH


2013/3/18 Jain, Nikhil <nikhil AT illinois.edu>
It appears that your MPI library is not in the linker path, and hence ld is not able to locate any of the functions required from MPI. Can you check the LD_LIBRARY_PATH environment variable.

--Nikhil

--
Doctoral Candidate @ CS, UIUC
 


From: Dimar Jaime González Soto <dimar.gonzalez.soto AT gmail.com>
Date: Monday, March 18, 2013 3:56 PM
To: Nikhil Jain <nikhil AT illinois.edu>, "charm AT cs.illinois.edu" <charm AT cs.illinois.edu>
Subject: Re: [charm] make pgm error
Resent-From: Nikhil Jain <nikhil AT illinois.edu>
Resent-Date: Mon, 18 Mar 2013 15:56:23 -0500

Thanks for the response Jain, as a like before I builded charm successfully.  I use the follow commmand line to build charm:

MPICXX=/shared/openmpi-1.6.4/bin/mpicxx ./build charm++ mpi-linux-x86_64 --with-production

next I go to:

cd mpi-linux-x86_64/tests/charm++/megatest

and write:

make pgm

the output:

../../../bin/../lib/libconv-cplus-y.a(machine.o): In function `CmiReplicaRecv':
machine.c:(.text+0x5d): undefined reference to `hpmp_byte'
../../../bin/../lib/libconv-cplus-y.a(machine.o): In function `CmiReplicaSend':
machine.c:(.text+0x84): undefined reference to `hpmp_byte'
../../../bin/../lib/libconv-cplus-y.a(machine.o): In function `CmiBarrierZero':
machine.c:(.text+0xe3): undefined reference to `hpmp_byte'
machine.c:(.text+0x14f): undefined reference to `hpmp_byte'
../../../bin/../lib/libconv-cplus-y.a(machine.o): In function `CmiReplicaSendrecv':
machine.c:(.text+0x36e): undefined reference to `hpmp_byte'
../../../bin/../lib/libconv-cplus-y.a(machine.o):machine.c:(.text+0x78a): more undefined references to `hpmp_byte' follow
../../../bin/../lib/libconv-cplus-y.a(machine.o): In function `CmiTimerInit':
machine.c:(.text+0xc1c): undefined reference to `hpmp_min'
machine.c:(.text+0xc23): undefined reference to `hpmp_double'
../../../bin/../lib/libconv-cplus-y.a(machine.o): In function `ConverseInit':
machine.c:(.text+0x11f4): undefined reference to `hpmp_comm_world'
machine.c:(.text+0x1328): undefined reference to `hpmp_comm_world'
machine.c:(.text+0x1471): undefined reference to `hpmp_comm_world'
machine.c:(.text+0x1482): undefined reference to `hpmp_comm_self'
../../../bin/../lib/libconv-cplus-y.a(machine.o): In function `CmiNotifyIdleForMPI':
machine.c:(.text+0x192f): undefined reference to `hpmp_byte'
machine.c:(.text+0x1961): undefined reference to `hpmp_byte'
collect2: ld returned 1 exit status
Fatal Error by charmc in directory /home/hpcadmin/software/NAMD_2.9_Source/charm-6.4.0/mpi-linux-x86_64/tests/charm++/megatest
   Command /shared/openmpi-1.6.4/bin/mpicxx -m64 -fPIC -DCMK_GFORTRAN -rdynamic -o pgm -L../../../bin/../lib -I../../../bin/../include ../../../bin/../lib/libldb-rand.o megatest.o groupring.o nodering.o varsizetest.o varsizetest2.o varraystest.o groupcast.o groupmulti.o groupsectiontest.o multisectiontest.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 bitvector.o immediatering.o callback.o inlineem.o completion_test.o moduleinit10933.o -lmodulecompletion ../../../bin/../lib/libmemory-default.o ../../../bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl -lmodulecompletion -lm returned error code 1
charmc exiting...



2013/3/18 Jain, Nikhil <nikhil AT illinois.edu>
Hi Dimar,

Unless I missed it completely, what you had pasted did not indicate why linking failed. Are you able to compile simple Charm++ program such as in $(CHARMDIR)/examples/charm++/hello. If yes, my suspects will be the location of fft/tcl installations. It will be helpful  if you can look at the error output again, and see if there is a print about why the linking failed. Also, can you paste the ./config command you had used for building NAMD.

--Nikhil


--
Doctoral Candidate @ CS, UIUC
 


From: Dimar Jaime González Soto <dimar.gonzalez.soto AT gmail.com>
Date: Monday, March 18, 2013 9:01 AM
To: "charm AT cs.illinois.edu" <charm AT cs.illinois.edu>
Subject: [charm] make pgm error
Resent-From: Nikhil Jain <nikhil AT illinois.edu>
Resent-Date: Mon, 18 Mar 2013 09:23:23 -0500

Dimar González Soto



--
Atte.

Dimar González Soto
Ingeniero Civil en Informática
Universidad Austral de Chile
F:+056-63-293858
www.australomics.cl






--
Atte.

Dimar González Soto
Ingeniero Civil en Informática
Universidad Austral de Chile
F:+056-63-293858
www.australomics.cl






--
Atte.

Dimar González Soto
Ingeniero Civil en Informática
Universidad Austral de Chile
F:+056-63-293858
www.australomics.cl







--
Atte.

Dimar González Soto
Ingeniero Civil en Informática
Universidad Austral de Chile
F:+056-63-293858
www.australomics.cl






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