Installing blacs libs: tester problems

[gortiz]

Hello,

Please, if you can help me with following compiling errors.
After compiling blacs Libs using g77-3.3 and using
BLACS/TESTING Makefile, I obtain:

================================================
( cd TESTING ; make )
make[1]: Entering directory `/home/gortiz/Blacs/BLACS/TESTING'
g77 -fno-globals -fno-f90 -fugly-complex -w -c blacstest.f
make mpif.h
make[2]: Entering directory `/home/gortiz/Blacs/BLACS/TESTING'
rm -f mpif.h
ln -s /opt/mpich/include/mpif.h mpif.h
make[2]: Leaving directory `/home/gortiz/Blacs/BLACS/TESTING'
g77 -c -O btprim_MPI.f
g77 -c tools.f
g77 -o /home/gortiz/Blacs/BLACS/TESTING/EXE/xFbtest_MPI-LINUX-0 blacstest.o btprim_MPI.o tools.o /home/gortiz/Blacs/BLACS/LIB/blacsF77init_MPI-LINUX-0.a /home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a /home/gortiz/Blacs/BLACS/LIB/blacsF77init_MPI-LINUX-0.a /opt/mpich/ch-p4mpd/lib64/libmpich.a
btprim_MPI.o: In function `btsetup_':
btprim_MPI.f:(.text+0x24): undefined reference to `mpi_initialized__'
btprim_MPI.f:(.text+0x38): undefined reference to `mpi_init__'
btprim_MPI.f:(.text+0x7a): undefined reference to `mpi_comm_dup__'
btprim_MPI.o: In function `ibtmyproc_':
btprim_MPI.f:(.text+0xc3): undefined reference to `mpi_comm_rank__'
btprim_MPI.o: In function `ibtnprocs_':
btprim_MPI.f:(.text+0x110): undefined reference to `mpi_comm_size__'
btprim_MPI.o: In function `btsend_':
btprim_MPI.f:(.text+0x229): undefined reference to `mpi_send__'
btprim_MPI.f:(.text+0x27f): undefined reference to `mpi_send__'
btprim_MPI.o: In function `btrecv_':
btprim_MPI.f:(.text+0x354): undefined reference to `mpi_recv__'
btprim_MPI.o: In function `ibtsizeof_':
btprim_MPI.f:(.text+0x3a5): undefined reference to `mpi_initialized__'
btprim_MPI.f:(.text+0x3bb): undefined reference to `mpi_init__'
btprim_MPI.f:(.text+0x505): undefined reference to `mpi_type_size__'
btprim_MPI.o: In function `btmpierr_':
btprim_MPI.f:(.text+0x5ab): undefined reference to `mpi_abort__'
btprim_MPI.o:(.data+0x0): undefined reference to `mpi_dup_fn__'
btprim_MPI.o:(.data+0x8): undefined reference to `mpi_null_delete_fn__'
btprim_MPI.o:(.data+0x10): undefined reference to `mpi_null_copy_fn__'
btprim_MPI.o:(.data+0x18): undefined reference to `mpi_dup_fn__'
btprim_MPI.o:(.data+0x20): undefined reference to `mpi_null_delete_fn__'
btprim_MPI.o:(.data+0x28): undefined reference to `mpi_null_copy_fn__'
btprim_MPI.o:(.data+0x30): undefined reference to `mpi_dup_fn__'
btprim_MPI.o:(.data+0x38): undefined reference to `mpi_null_delete_fn__'
btprim_MPI.o:(.data+0x40): undefined reference to `mpi_null_copy_fn__'
btprim_MPI.o:(.data+0x48): undefined reference to `mpi_dup_fn__'
btprim_MPI.o:(.data+0x50): undefined reference to `mpi_null_delete_fn__'
btprim_MPI.o:(.data+0x58): undefined reference to `mpi_null_copy_fn__'
btprim_MPI.o:(.data+0x60): undefined reference to `mpi_dup_fn__'
btprim_MPI.o:(.data+0x68): undefined reference to `mpi_null_delete_fn__'
btprim_MPI.o:(.data+0x70): undefined reference to `mpi_null_copy_fn__'
btprim_MPI.o:(.data+0x78): undefined reference to `mpi_dup_fn__'
btprim_MPI.o:(.data+0x80): undefined reference to `mpi_null_delete_fn__'
btprim_MPI.o:(.data+0x88): undefined reference to `mpi_null_copy_fn__'
btprim_MPI.o:(.data+0x90): undefined reference to `mpi_dup_fn__'
btprim_MPI.o:(.data+0x98): undefined reference to `mpi_null_delete_fn__'
btprim_MPI.o:(.data+0xa0): undefined reference to `mpi_null_copy_fn__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_get_constants.o):(.data+0x0): undefined reference to `mpi_conversion_fn_null__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_get_constants.o):(.data+0x8): undefined reference to `mpi_type_null_copy_fn__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_get_constants.o):(.data+0x10): undefined reference to `mpi_type_null_delete_fn__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_get_constants.o):(.data+0x18): undefined reference to `mpi_type_dup_fn__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_get_constants.o):(.data+0x20): undefined reference to `mpi_win_null_copy_fn__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_get_constants.o):(.data+0x28): undefined reference to `mpi_win_null_delete_fn__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_get_constants.o):(.data+0x30): undefined reference to `mpi_win_dup_fn__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_get_constants.o):(.data+0x38): undefined reference to `mpi_comm_null_copy_fn__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_get_constants.o):(.data+0x40): undefined reference to `mpi_comm_null_delete_fn__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_get_constants.o):(.data+0x48): undefined reference to `mpi_comm_dup_fn__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_get_constants.o):(.data+0x50): undefined reference to `mpi_null_copy_fn__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_get_constants.o):(.data+0x58): undefined reference to `mpi_null_delete_fn__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_get_constants.o):(.data+0x60): undefined reference to `mpi_dup_fn__'
/home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a(bi_f77_init.o): In function `bi_f77_init__':
bi_f77_init.f:(.text+0xf): undefined reference to `mpi_init__'
collect2: ld returned 1 exit status
make[1]: *** [/home/gortiz/Blacs/BLACS/TESTING/EXE/xFbtest_MPI-LINUX-0] Error 1
make[1]: Leaving directory `/home/gortiz/Blacs/BLACS/TESTING'
make: *** [tester] Error 2

====================================================


Thanks a lot,

g.

[Julie]

gortiz,
Could you try the ScaLAPACK installer from netlib.
You can find it on the ScaLAPACK webpage: http://www.netlib.org/scalapack .
Julie

[gortiz]

Hello Julie,

Yes, I did it, but there says that:
"Assumes the BLAS, the BLACS and the LAPACK are available."
Thus, I folow the links to libs BLACS in http://www.netlib.org/blacs/.
I try to build it, and then I obtain the problems described above.

It does sense for you?

Thanks you for help me.

g.

[Julie]

What is your setup command and the output and log of the installer?

The installer will download and install everything for you if you use the following command:
./setup.py --downblas --downlapack --downblacs

I can tell by the compile output that you did not use the installer. You have to use mpicc and mpif77 to compile.

g77 -o /home/gortiz/Blacs/BLACS/TESTING/EXE/xFbtest_MPI-LINUX-0 blacstest.o btprim_MPI.o tools.o /home/gortiz/Blacs/BLACS/LIB/blacsF77init_MPI-LINUX-0.a /home/gortiz/Blacs/BLACS/LIB/blacs_MPI-LINUX-0.a /home/gortiz/Blacs/BLACS/LIB/blacsF77init_MPI-LINUX-0.a /opt/mpich/ch-p4mpd/lib64/libmpich.a

Julie
Julie

[gortiz]

Ups..

Then, If I understanding you, the installer that you say build also
blacs libs for me!! For example: blacsF77init_MPI-LINUX-0.a
that I trying to build before to trying to build scalapack, is not it?

If it is the case, I did not understand why in
http://www.netlib.org/scalapack/ says that assumes that
lapack, blacs, and blas are available?

OK, thank you again for help me to learn about it.

g.

[Julie]

Then, If I understanding you, the installer that you say build also blacs libs for me!! For example: blacsF77init_MPI-LINUX-0.a that I trying to build before to trying to build scalapack, is not it?

Yes!

ScaLAPACK and the ScaLAPACK installer are two different things.
- ScaLAPACK contains only the ScaLAPACK library! It is up to the user to download and install correctly the required libraries (BLAS, LAPACK and BLACS) by himself.
- The ScaLAPACK installer is just a set of scripts to ease the installation of ScaLAPACK. It will download everything for you if you ask him (BLAS, LAPACK and BLACS) and it will try to install all the libraries correctly.

Hope it make sense,
Julie

[gortiz]

OK Julie,

Just I find the document
http://www.netlib.org/scalapack/scalapa ... .91/README

I will try to use scalapack installer and I will return to you
with my report of it.

Thanks a lot,

g.

[gortiz]

HI Julie,

Let me say you that installer script for scalapack is great!
I can build scalapack libs on my desktop AMD 64 bit Athlon computer
and now I am doing testing of it.

But, also, I am trying to build using same script in other machine
that actually will do calculation on multiple procesors. Then, I realize
that setup.py script did not ask me for mpi libs location !!
I mean, with --mpibindir and --mpiincludedir I can pass the
path to installed mpi binaries and include files, but what about libs
as for example libmpich?

Here the output when I trying to install there using scalapack_installer

./setup.py --mpibindir=/usr/local/mpich2/bin --mpiincdir=/usr/local/mpich2/include --blaslib=/usr/lib64/libblas.a --downblacs --downlapack
========================================
Setting up the framework

MPI bin dir is /usr/local/mpich2/bin
MPI include dir is /usr/local/mpich2/include
mpicc : /usr/local/mpich2/bin/mpicc
mpif77 : /usr/local/mpich2/bin/mpif77
Checking if mpicc works...

COMMON: mpicc not working! aborting...
stderr:
****************************************
/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/bin/ld: cannot find -lmpich
collect2: ld returned 1 exit status
=======================================

Surprise me that this problem did not appear when I did
almost the same on my desktop computer...

Best regards.

g.

[Julie]

Below is the code that the installer tried:

Code: Select all

            #include "mpi.h"
            #include <stdio.h>
            int main(int argc, char **argv){
            int iam;
            MPI_Init( &argc, &argv );
            MPI_Comm_rank( MPI_COMM_WORLD, &iam );
            if(iam==0){fprintf(stdout, "success" );fflush(stdout);}
            MPI_Finalize();
            return 0;
            }

and the compilation command:

Code: Select all

        /usr/local/mpich2/bin/mpicc -o tmpc tmpc.c

I think your mpi installation has a problem and this is why the ScaLAPACK installer fails.
Try to compile the above program with the link command.
I think you will get the same error message that you have.
I will suggest to reinstall properly mpich2 on that machine.

Julie

[gortiz]

Thank you Julie,

Yes, I obtain the same. And when I run:

"/usr/local/mpich2/bin/mpicc -o tmpc tmpc.c -L/usr/local/mpich2/lib -lmpich"

I have

"/tmp/ccNjhSli.o: In function `main':
tmpc.c:(.text+0x21): undefined reference to `lam_mpi_comm_world'
collect2: ld returned 1 exit status"

Then, I think that there mpi is lam and not mpich2

Then, I change option for scalapack_installer:

./setup.py --mpibindir=/usr/local/bin --mpiincdir=/usr/local/include --blaslib=/usr/lib64/libblas.a --lapacklib=/usr/lib64/liblapack.a --downblacs --downlapack
========================================
Setting up the framework

MPI bin dir is /usr/local/bin
MPI include dir is /usr/local/include
mpicc : /usr/local/bin/mpicc
mpif77 : /usr/local/bin/mpif77
Checking if mpicc works...

COMMON: mpicc not working! aborting...
error is:
****************************************
-----------------------------------------------------------------------------

It seems that there is no lamd running on the host nodo0.

This indicates that the LAM/MPI runtime environment is not operating.
The LAM/MPI runtime environment is necessary for MPI programs to run
(the MPI program tired to invoke the "MPI_Init" function).

Please run the "lamboot" command the start the LAM/MPI runtime
environment. See the LAM/MPI documentation for how to invoke
"lamboot" across multiple machines.
-----------------------------------------------------------------------------

Seems that I need to run some demon for lam, is not it ?

Thanks you again,

g.

[ltaief]

There is a good tutorial on the lammpi website which explains what to do before running the actual application:

http://www.lam-mpi.org/tutorials/one-step/lam.php


Hope this helps!

Hatem

[gortiz]

Hello everybody

Thanks a lot by scalapack_installer
and all supporting aids that you gave me.

All seems to work fine. And I hope contribute
on more interesting questions for you in the future
using it.

And also for excusing me my short grammar

Thanks

guillermo.

[yamen]

Plz I am facing the same error that gortiz have written at first and I am using ScaLAPACK installer. if only one can give me the reuired flags
I am using GNU compiler for fortran and C and I am working on arch = Linux, comm = MPI, CPU= x86_64

[gortiz]

Hi Yamen,

If you have the last problem that I have reported,
then you need only to run lamboot. For example,
in my case it was:

lamboot -v /usr/local/etc/lam-bhost.def

where "/usr/local/etc/lam-bhost.def" contains
list of name of nodes of your cluster, for example:

node0
node1
node2
........

I recomend you to see manuals for bhost y lamboot.

But if you problem is not related, please, let me know
what it is. And I will try to helo you.

g.

[yamen]

i am afraid that my problem is not related.

:)