ScaLAPACK Archives

[Scalapack] BUG'SSS REPORTSS

Hi,
For 1, you did not link correctly,

For 2, Change in the install script file: script/lapack.py at line 258
from
        os.chdir(os.path.join(os.getcwd(),'lapack-3.4.1'))
to
        os.chdir(os.path.join(os.getcwd(),'lapack-3.4.2'))

I will make the correction in the installer.
Now it should work.
Once your install work with Reference BLAS, you are good to go. you will have 
just to link with your own BLAS with your programs,
Julie
On Oct 25, 2012, at 2:41 AM, Joni-Pekka Kurronen <joni.kurronen@Domain.Removed> 
wrote:


hi,

I try to get installed mpich2, ..... up to elmerfem / OpenFOAM / netgen to
 /mpi4 directory to be run parrallel,...

Have problems to get Scalap work at
https://sites.google.com/site/jpsdatareviewstheboy007/ubuntu-lts-12-4-companion-whit-ltsp-mpich2-elmer-openfoam

system:
  -ubuntu 12.4 LTS
  -mpich2
  - latest AMD amcl ( gfortran_mp )

Problems Whit source installation:

1.  see attached files, this comes out whit make:
============
Linking Fortran executable cpb1tst
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(cgemvTcomp.o): In 
function `cgemvtcomp_':
cgemvTcomp.f:(.text+0x270): undefined reference to `GOMP_parallel_start'
cgemvTcomp.f:(.text+0x27f): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(cherk.o): In function 
`cherk_._omp_fn.3':
cherk.F:(.text+0x6f): undefined reference to `omp_get_num_threads'
cherk.F:(.text+0x7b): undefined reference to `omp_get_thread_num'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(cherk.o): In function 
`cherk_._omp_fn.2':
cherk.F:(.text+0x32c): undefined reference to `omp_get_num_threads'
cherk.F:(.text+0x335): undefined reference to `omp_get_thread_num'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(cherk.o): In function 
`cherk_._omp_fn.1':
cherk.F:(.text+0x5b9): undefined reference to `omp_get_num_threads'
cherk.F:(.text+0x5c5): undefined reference to `omp_get_thread_num'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(cherk.o): In function 
`cherk_._omp_fn.0':
cherk.F:(.text+0x854): undefined reference to `omp_get_num_threads'
cherk.F:(.text+0x860): undefined reference to `omp_get_thread_num'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(cherk.o): In function 
`cherk_':
cherk.F:(.text+0xdef): undefined reference to `GOMP_parallel_start'
cherk.F:(.text+0xe01): undefined reference to `GOMP_parallel_end'
cherk.F:(.text+0x1800): undefined reference to `GOMP_parallel_start'
cherk.F:(.text+0x1812): undefined reference to `GOMP_parallel_end'
cherk.F:(.text+0x195e): undefined reference to `GOMP_parallel_start'
cherk.F:(.text+0x1970): undefined reference to `GOMP_parallel_end'
cherk.F:(.text+0x1a55): undefined reference to `GOMP_parallel_start'
cherk.F:(.text+0x1a67): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(csyrk.o): In function 
`csyrk_._omp_fn.3':
csyrk.F:(.text+0x6c): undefined reference to `omp_get_num_threads'
csyrk.F:(.text+0x78): undefined reference to `omp_get_thread_num'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(csyrk.o): In function 
`csyrk_._omp_fn.2':
csyrk.F:(.text+0x319): undefined reference to `omp_get_num_threads'
csyrk.F:(.text+0x322): undefined reference to `omp_get_thread_num'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(csyrk.o): In function 
`csyrk_._omp_fn.1':
csyrk.F:(.text+0x5a6): undefined reference to `omp_get_num_threads'
csyrk.F:(.text+0x5b2): undefined reference to `omp_get_thread_num'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(csyrk.o): In function 
`csyrk_._omp_fn.0':
csyrk.F:(.text+0x831): undefined reference to `omp_get_num_threads'
csyrk.F:(.text+0x83d): undefined reference to `omp_get_thread_num'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(csyrk.o): In function 
`csyrk_':
csyrk.F:(.text+0x10e8): undefined reference to `GOMP_parallel_start'
csyrk.F:(.text+0x10fa): undefined reference to `GOMP_parallel_end'
csyrk.F:(.text+0x11c5): undefined reference to `GOMP_parallel_start'
csyrk.F:(.text+0x11d7): undefined reference to `GOMP_parallel_end'
csyrk.F:(.text+0x12f3): undefined reference to `GOMP_parallel_start'
csyrk.F:(.text+0x1305): undefined reference to `GOMP_parallel_end'
csyrk.F:(.text+0x13c2): undefined reference to `GOMP_parallel_start'
csyrk.F:(.text+0x13d4): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(ompaax.o): In function 
`ompaax_':
ompaax.F:(.text+0x7): undefined reference to `omp_get_thread_num_'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(ompaay.o): In function 
`ompaay_':
ompaay.F:(.text+0x7): undefined reference to `omp_get_num_threads_'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(ompaaz.o): In function 
`ompaaz_._omp_fn.0':
ompaaz.F:(.text+0x7): undefined reference to `omp_get_num_threads_'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(ompaaz.o): In function 
`ompaaz_':
ompaaz.F:(.text+0x28): undefined reference to `GOMP_parallel_start'
ompaaz.F:(.text+0x35): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(cgemmcomp.o): In function 
`cgemmcomp2_':
cgemmcomp.f:(.text+0x1bc): undefined reference to `GOMP_barrier'
cgemmcomp.f:(.text+0x462): undefined reference to `GOMP_barrier'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(cgemmcomp.o): In function 
`cgemmcomp_':
cgemmcomp.f:(.text+0x28dd): undefined reference to `GOMP_parallel_start'
cgemmcomp.f:(.text+0x28ec): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(cgemvCcomp.o): In 
function `cgemvccomp_':
cgemvCcomp.f:(.text+0x270): undefined reference to `GOMP_parallel_start'
cgemvCcomp.f:(.text+0x27f): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(cgemvNcomp.o): In 
function `cgemvncomp_':
cgemvNcomp.f:(.text+0x199): undefined reference to `GOMP_parallel_start'
cgemvNcomp.f:(.text+0x1a8): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(cgerccomp.o): In function 
`cgerccomp_':
cgerccomp.f:(.text+0x248): undefined reference to `GOMP_parallel_start'
cgerccomp.f:(.text+0x257): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(cgerucomp.o): In function 
`cgerucomp_':
cgerucomp.f:(.text+0x248): undefined reference to `GOMP_parallel_start'
cgerucomp.f:(.text+0x257): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(chemmcomp.o): In function 
`chemmcomp_._omp_fn.0':
chemmcomp.f:(.text+0xa2): undefined reference to `GOMP_barrier'
chemmcomp.f:(.text+0x1b5): undefined reference to `GOMP_barrier'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(chemmcomp.o): In function 
`chemmcomp_':
chemmcomp.f:(.text+0x363): undefined reference to `GOMP_parallel_start'
chemmcomp.f:(.text+0x370): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(csymmcomp.o): In function 
`csymmcomp_._omp_fn.0':
csymmcomp.f:(.text+0x92): undefined reference to `GOMP_barrier'
csymmcomp.f:(.text+0x191): undefined reference to `GOMP_barrier'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(csymmcomp.o): In function 
`csymmcomp_':
csymmcomp.f:(.text+0x333): undefined reference to `GOMP_parallel_start'
csymmcomp.f:(.text+0x340): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(ctrmmL.o): In function 
`ctrmml_._omp_fn.0':
ctrmmL.f:(.text+0xca): undefined reference to `GOMP_barrier'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(ctrmmL.o): In function 
`ctrmml_':
ctrmmL.f:(.text+0xe81): undefined reference to `GOMP_parallel_start'
ctrmmL.f:(.text+0xe8e): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(ctrmmU.o): In function 
`ctrmmu_._omp_fn.0':
ctrmmU.f:(.text+0xc7): undefined reference to `GOMP_barrier'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(ctrmmU.o): In function 
`ctrmmu_':
ctrmmU.f:(.text+0xe5c): undefined reference to `GOMP_parallel_start'
ctrmmU.f:(.text+0xe69): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(ctrsmL.o): In function 
`ctrsml_._omp_fn.0':
ctrsmL.f:(.text+0xc7): undefined reference to `GOMP_barrier'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(ctrsmL.o): In function 
`ctrsml_':
ctrsmL.f:(.text+0xe56): undefined reference to `GOMP_parallel_start'
ctrsmL.f:(.text+0xe63): undefined reference to `GOMP_parallel_end'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(ctrsmU.o): In function 
`ctrsmu_._omp_fn.0':
ctrsmU.f:(.text+0xc2): undefined reference to `GOMP_barrier'
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a(ctrsmU.o): In function 
`ctrsmu_':
ctrsmU.f:(.text+0xf05): undefined reference to `GOMP_parallel_start'
ctrsmU.f:(.text+0xf12): undefined reference to `GOMP_parallel_end'
collect2: ld:n paluuarvo oli 1
make[2]: *** [PBLAS/TESTING/cpb1tst] Virhe 1
make[1]: *** [PBLAS/TESTING/CMakeFiles/cpb1tst.dir/all] Virhe 2
make: *** [all] Virhe 2


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


Whit install script:

1. if mpirun set mpicxx   dose get mpi error's
=======
/tmpc:(.dtors+0x8): first defined here
/usr/bin/ld: error in ./tmpc(.eh_frame); no .eh_frame_hdr table will be 
created.
collect2: ld:n paluuarvo oli 1
=======

2. when remove  --mpirun=[command]
I can proceed but BUILD IN LAPACK can not be found
=========
========================================
 BLAS installation/verification
========================================
Checking if the provided LAPACK 
(/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a) contains BLAS
BLAS library is set to /mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a
Checking if provided BLAS works... yes
Which BLAS library do you want to use ?
   - b : the BLAS library you requested: 
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a
   - l : the LAPACK library you provided: 
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a
[l] b
BLAS library is set to /mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a
Checking if provided BLAS works... yes

========================================
 Lapack installation/verification
========================================
LAPACK library is /mpi4/C_MP/acml5.2.0/g
=========


3. IF INSTALL LAPACK IT HAS DIRECTORY NOt REGONIZED
=======
   self.down_install_lapack()
 File "/mpi4/S/scalapack_installer_1.0.2/script/lapack.py", line 258, in 
down_install_lapack
   os.chdir(os.path.join(os.getcwd(),'lapack-3.4.1'))
OSError: [Errno 2] No such file or directory: 
'/mpi4/S/scalapack_installer_1.0.2/build/lapack-3.4.1'
joni at mpi1:/mpi4/S/scalapack_installer_1.0.2$ ls
build  history.log  LICENSE  netlib.py  netlib.pyc  README  script setup.py
joni at mpi1:/mpi4/S/scalapack_installer_1.0.2$ ls build
download  lapack-3.4.2  log  scalapack-2.0.2  tmpf.f
=======


-- 

Joni-Pekka Kurronen
AMRINA, Insin??ri AMK veneala

==

========================================
 BLAS installation/verification
========================================
Checking if the provided LAPACK 
(/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a) contains BLAS
BLAS library is set to /mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a
Checking if provided BLAS works... yes
Which BLAS library do you want to use ?
   - b : the BLAS library you requested: 
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a
   - l : the LAPACK library you provided: 
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a
[l] b
BLAS library is set to /mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a
Checking if provided BLAS works... yes

========================================
 Lapack installation/verification
========================================
LAPACK library is /mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.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] q
joni at mpi1:/mpi4/S/scalapack_installer_1.0.2$ ./setup.py 
--prefix=$SCALAPACK --mpibindir=$JPK_MPICH2/bin --mpicc=mpicc --mpif90=mpif90 
--mpiincdir=$JPK_MPICH2/include --ccflags="-O3 -fPIC" --fcflags="-O3 -fPIC" 
--blaslib=$BLAS/lib/libacml_mp.a --lapacklib=$BLAS/lib/libacml_mp.a
========================================
Setting up the framework
ScaLAPACK installer version (1, 0, 2)
MPI bin dir is  /mpi4/C_MP/mpich2-1.5/bin
mpicc is  mpicc
mpif90 is  mpif90
MPI include dir is  /mpi4/C_MP/mpich2-1.5/include
C flags are  -O3 -fPIC
Fortran flags are  -O3 -fPIC
Install directory is... /mpi4/C_MP/scalapack-2.0.2
Build directory is... /mpi4/S/scalapack_installer_1.0.2/build
BLAS library is...  /mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a
LAPACK library is...  /mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a
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... working
Setting ranlib command... /usr/bin/ranlib
Detecting Fortran compiler... unknown
Detecting C compiler... unknown
C flags are...  -O3 -fPIC
Fortran flags are...  -O3 -fPIC
Selected loader flags (C main):
Selected loader flags (f90 main):
Selected NOOPT flags: -O0
AR flags are...  rc
Checking loader... works

========================================
 BLAS installation/verification
========================================
Checking if the provided LAPACK 
(/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a) contains BLAS
BLAS library is set to /mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a
Checking if provided BLAS works... yes
Which BLAS library do you want to use ?
   - b : the BLAS library you requested: 
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a
   - l : the LAPACK library you provided: 
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a
[l]
Using the BLAS library contained in LAPACK library 
/mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.a

========================================
 Lapack installation/verification
========================================
LAPACK library is /mpi4/C_MP/acml5.2.0/gfortran64_mp/lib/libacml_mp.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... Creating directory 
/mpi4/S/scalapack_installer_1.0.2/build/download
done
Unzip and untar reference LAPACK... done
Traceback (most recent call last):
 File "./setup.py", line 51, in <module>
   sys.exit(main(sys.argv))
 File "./setup.py", line 44, in main
   Lapack(config, scalapack);
 File "/mpi4/S/scalapack_installer_1.0.2/script/lapack.py", line 78, in 
__init__
   self.down_install_lapack()
 File "/mpi4/S/scalapack_installer_1.0.2/script/lapack.py", line 258, in 
down_install_lapack
   os.chdir(os.path.join(os.getcwd(),'lapack-3.4.1'))
OSError: [Errno 2] No such file or directory: 
'/mpi4/S/scalapack_installer_1.0.2/build/lapack-3.4.1'
joni at mpi1:/mpi4/S/scalapack_installer_1.0.2$ ls
build  history.log  LICENSE  netlib.py  netlib.pyc  README  script  setup.py
joni at mpi1:/mpi4/S/scalapack_installer_1.0.2$ ls build
download  lapack-3.4.2  log  scalapack-2.0.2  tmpf.f
joni at mpi1:/mpi4/S/scalapack_installer_1.0.2$

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