ScaLAPACK: error building ScaLAPACK test routines

Post here if you have some questions about the ScaLAPACK installer

ScaLAPACK: error building ScaLAPACK test routines

Postby bencat » Wed Feb 08, 2012 1:38 pm

I try to install ScaLAPACK by scalapack_installer.

I used "./setup.py --blaslib="/home/lchen/myroot/lib/libf77blas.a /home/lchen/myroot/lib/libatlas.a" --prefix=$HOME/myroot" to setup.
The LAPACK works well, but the testing of scalapack doesn't.

========================================
Setting up the framework
ScaLAPACK installer version (1, 0, 1)
Install directory is... /home/lchen/myroot
Build directory is... /home/lchen/scalapack_installer_1.0.1/build
Looking for MPI binaries... mpicc, mpif90 and mpirun found.
mpicc : /home/rge/mpich2-1.4/BUILD/bin/mpicc
mpif90 :/home/rge/mpich2-1.4/BUILD/bin/mpif90
mpirun :/home/rge/mpich2-1.4/BUILD/bin/mpirun
Looking for mpi.h... found in /home/rge/mpich2-1.4/BUILD/include
BLAS library is... /home/lchen/myroot/lib/libf77blas.a /home/lchen/myroot/lib/libatlas.a
LAPACK library is... Check if included in Blas library
Checking if mpicc works... yes
Checking if mpirun works... yes
Checking if mpif90 works... yes
Setting Fortran mangling... -DAdd_
Setting download command...
Checking availability of urllib... available
Testing urllib... not working
Checking availablility of wget... available
Testing wget... not working.
Setting ranlib command... /usr/bin/ranlib
Detecting Fortran compiler... unknown
Detecting C compiler... GNU
C flags are... -O2
Fortran flags are... -O2
Selected loader flags (C main):
Selected loader flags (f90 main):
Selected NOOPT flags: -O0
AR flags are... rc
Checking loader... works

========================================
BLAS installation/verification
========================================
BLAS library is set to /home/lchen/myroot/lib/libf77blas.a /home/lchen/myroot/lib/libatlas.a
Checking if provided BLAS works... yes

========================================
Lapack installation/verification
========================================
LAPACK library is set to /home/lchen/myroot/lib/libf77blas.a /home/lchen/myroot/lib/libatlas.a
Checking if provided LAPACK works... no

Please provide a working LAPACK library. If a LAPACK library is not
present on the system, the netlib LAPACK library can be automatically
downloaded and installed by adding the --downlapack flag.
Most used BLAS implementations already include the LAPACK library as
MKL, ACML, Goto, Goto2 or ATLAS. If you want to use one of these
libraries, you just have to specify correctly the --blaslib option or
you can specify where is located your own LAPACK library by using the
--lapacklib option.

With LAPACK, netlib require also the tmglib from LAPACK which is only
included in MKL and netlib LAPACK (--lapacklib=-ltmg -llapack). For
other BLAS libraries, LAPACK will be automatically downloaded from
netlib.

The LAPACK library is not needed in the case where testing is disabled
by means of the --notesting flag.


What do you want to do ?
- d : download the netlib LAPACK
- q : quit and try with another BLAS library or define the
lapacklib parameter.

>[q] d
The reference LAPACK library is being installed.
Downloading reference LAPACK... (package ./lapack.tgz already downloaded)... done
Unzip and untar reference LAPACK... done
Compile and generate LAPACK... done
Installation of libreflapack.a successful.
(log is in /home/lchen/scalapack_installer_1.0.1/build/log/lapacklog )
Compiling and Running LAPACK test suite (this will take several minutes)... done
(log is in /home/lchen/scalapack_installer_1.0.1/build/log/lapack_testing )
LAPACK library is -L/home/lchen/myroot/lib -ltmg -lreflapack
Checking if provided LAPACK works... yes
Getting LAPACK version number... 3.4.0
Checking if provided LAPACK contains functions for test works... yes

========================================
ScaLAPACK installer is starting now. Buckle up!
========================================
Downloading ScaLAPACK... (package ./scalapack.tgz already downloaded)... done
Installing scalapack-2.0.1 ...
Writing SLmake.inc... done.
Compiling BLACS, PBLAS and ScaLAPACK... done
Getting ScaLAPACK version number... 2.0.1
Installation of ScaLAPACK successful.
(log is in /home/lchen/scalapack_installer_1.0.1/build/log/scalog )
Compiling test routines...

ScaLAPACK: error building ScaLAPACK test routines
stderr:
****************************************
/home/lchen/myroot/lib/libreflapack.a(xerbla.o): In function `xerbla_':
xerbla.f:(.text+0x66): undefined reference to `_gfortran_transfer_character_write'
xerbla.f:(.text+0x76): undefined reference to `_gfortran_transfer_integer_write'
collect2: ld returned 1 exit status
make[1]: *** [xspblas1tst] Error 1
make: *** [pblasexe] Error 2


I added -lgfortran in SLmake.in and make in the /scalapack, get the following error:
/usr/bin/ranlib ../libscalapack.a
make[1]: Leaving directory `/home/lchen/scalapack_installer_1.0.1/build/scalapack-2.0.1/SRC'
( cd BLACS; make tester )
make[1]: Entering directory `/home/lchen/scalapack_installer_1.0.1/build/scalapack-2.0.1/BLACS'
( cd TESTING ; make )
make[2]: Entering directory `/home/lchen/scalapack_installer_1.0.1/build/scalapack-2.0.1/BLACS/TESTING'
make[2]: Nothing to be done for `exe'.
make[2]: Leaving directory `/home/lchen/scalapack_installer_1.0.1/build/scalapack-2.0.1/BLACS/TESTING'
make[1]: Leaving directory `/home/lchen/scalapack_installer_1.0.1/build/scalapack-2.0.1/BLACS'
( cd PBLAS/TESTING; make single double complex complex16 )
make[1]: Entering directory `/home/lchen/scalapack_installer_1.0.1/build/scalapack-2.0.1/PBLAS/TESTING'
/home/rge/mpich2-1.4/BUILD/bin/mpif90 -o xspblas1tst psblas1tst.o psblastst.o slamch.o pblastst.o PB_Cwarn.o PB_Cabort.o ../../libscalapack.a -L/home/lchen/myroot/lib -ltmg -lreflapack /home/lchen/myroot/lib/libf77blas.a /home/lchen/myroot/lib/libatlas.a -lgfortran
/home/lchen/myroot/lib/libreflapack.a(xerbla.o): In function `xerbla_':
xerbla.f:(.text+0x66): undefined reference to `_gfortran_transfer_character_write'
xerbla.f:(.text+0x76): undefined reference to `_gfortran_transfer_integer_write'
collect2: ld returned 1 exit status
make[1]: *** [xspblas1tst] Error 1
make[1]: Leaving directory `/home/lchen/scalapack_installer_1.0.1/build/scalapack-2.0.1/PBLAS/TESTING'
make: *** [pblasexe] Error 2


The same error when I was installing.
Any tips would be helpful.
Thanks.
bencat
 
Posts: 1
Joined: Wed Feb 08, 2012 12:53 pm

Re: ScaLAPACK: error building ScaLAPACK test routines

Postby admin » Wed Feb 08, 2012 2:31 pm

Hi,
It seems to be a gfortran issue.
Just google "undefined reference to `_gfortran_transfer_character_write'" and you will see that many people have the same problem.
Gfortran has lost back-compatibility with the 4.5 in the 4.6 release on few very basic functions.
Best would be to recompile everything (mpich2, scalapack, etc..) with the latest gfortran release.
Sorry for the bad news.
Julie
admin
Site Admin
 
Posts: 498
Joined: Wed Dec 08, 2004 7:07 pm


Return to ScaLAPACK installer

Who is online

Users browsing this forum: No registered users and 1 guest