CP2K compilation errors
Eric Shamay
eric.... at gmail.com
Wed May 30 00:37:08 UTC 2007
I've managed to get the entire program to compile. Here are the
pertinent stats of the system:
firstly, my arch file
---------------------------------------------
PERL = perl
CC = mpicc
CPP = cpp
FC = mpif90 -FR
FC_fixed = mpif90 -FI
LD = mpif90
AR = ar -r
MKLPATH = $(MKL)/lib/64
DFLAGS = -D__INTEL -D__FFTSG -D__FFTW3 -D__parallel -D__BLACS -
D__SCALAPACK -D__FFTMKL -I$(FFTW)/include -I$(MKL)/include
CPPFLAGS = -C $(DFLAGS) -P -traditional
FCFLAGS = -O2 -Vaxlib -tpp2
LDFLAGS = $(FCFLAGS) -L$(HOME)/lib -L$(FFTW)/lib -L$(MPI)/lib -L$
(MKL)/lib/64
#LIBS = -lmkl_scalapack -lmkl_blacsF77init -lmkl_blacs\
# -lmkl_lapack -lmkl -lguide -lmpi -lfftw3
LIBS = $(MKLPATH)/libmkl_blacs.a\
$(MKLPATH)/libmkl_scalapack.a\
$(MKLPATH)/libmkl_blacsF77init.a\
$(MKLPATH)/libmkl_lapack.a\
$(MKLPATH)/libmkl_blacs_intelmpi.a\
$(MKLPATH)/libguide.a\
-lpthread -lmpi -lmkl -lfftw3
OBJECTS_ARCHITECTURE = machine_intel.o
---------------------------------------------
intel/9.1 (for the compilers)
> mpif90 -V
Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications
Version 9.1 Build 20070320 Package ID: <installpackageid>
>mpicc -V
Intel(R) C Itanium(R) Compiler for Itanium(R)-based applications
Version 9.1 Build 20070320 Package ID: <installpackageid>
mkl/7.2cluster_64
fftw/3.1.1
mpi/openmpi-1.1.5_intel-9.1
This setup finishes through the entire compilation and exits without
error. I then attempt to run a test as per the INSTALL file but by
running the command:
> mpirun -np 8 $PATH_TO_CP2KEXE H2O.inp > H2O.out
and the program produces the following output:
--------------------------------------------------------------------------------------------------------------------------------------------
username at optix has created process number
0 14411
username at optix has created process number
1 14412
username at optix has created process number
2 14413
username at optix has created process number
3 14414
username at optix has created process number
4 14415
username at optix has created process number
5 14416
username at optix has created process number
6 14417
username at optix has created process number
7 14418
**** **** ****** ** PROGRAM STARTED AT Tue May 29
17:26:39 2007
***** ** *** *** ** PROGRAM STARTED
ON optix
** **** ****** PROGRAM STARTED
BY username
***** ** ** ** ** PROGRAM PROCESS
ID 14411
**** ** ******* ** PROGRAM STARTED IN /mnt/netapp/home/users/
eshamay/tmp/cp
2k/tests/QS
CP2K| Program compiled at Tue May 29
17:12:39 PDT 2007
CP2K| Program compiled
on optix
CP2K| Program compiled for Linux-
ia64-intel
CP2K| Last CVS entry ur_center_integrals.F/1.19/Fri May 18
22:07:04 200
CP2K| Input file
name H2O.inp
GLOBAL| Force Environment
number 1
GLOBAL| Basis set file name
BASIS_SET
GLOBAL| Potential file name
POTENTIAL
GLOBAL| MM Potential file name
MM_POTENTIAL
GLOBAL| Restart file
name RESTART
GLOBAL| Coordinate file
name UNSET
GLOBAL| Method
name CP2K
GLOBAL| Project
name H2O
GLOBAL| Default FFT
library FFTW3
GLOBAL| Run
type MD
GLOBAL| All-to-all communication in single
precision F
GLOBAL| Global print
level 1
GLOBAL| Total number of message passing
processes 8
GLOBAL| Number of threads for this
process 1
GLOBAL| This output is from
process 0
6 additional processes aborted (not shown)
--------------------------------------------------------------------------------------------------------------------------------------------
This is followed by a series of mpi segfault/crash error that look
like :
17:35:12 eshamay at optix (~/tmp/cp2k/tests/QS) Signal:11 info.si_errno:
0(Success) si_code:2(SEGV_ACCERR)
Failing at addr:0xf3
[0] func:/usr/local/packages/openmpi/1.1_intel-9.1/lib/libopal.so.0
[0x200000000044c800]
[1] func:[0xa0000000000107e0]
[2] func:/usr/local/packages/openmpi/1.1_intel-9.1/lib/libmpi.so.0
[0x2000000000182dd0]
[3] func:/usr/local/packages/openmpi/1.1_intel-9.1/lib/libmpi.so.
0(MPI_Comm_size-0x9d3c20) [0x2000000000182c20]
[4] func:/home/users/eshamay/tmp/cp2k/exe/Linux-ia64-intel/
cp2k.popt(Cblacs_pinfo+0x2000000001798240) [0x40000000022eea90]
[5] func:/home/users/eshamay/tmp/cp2k/exe/Linux-ia64-intel/
cp2k.popt(blacs_gridmap_+0x2000000001140bb0) [0x4000000001c97410]
[6] func:/home/users/eshamay/tmp/cp2k/exe/Linux-ia64-intel/
cp2k.popt(blacs_gridinit_+0x20000000011409d0) [0x4000000001c97240]
<snip>
*** End of error message ***
6] func:/home/users/eshamay/tmp/cp2k/exe/Linux-ia64-intel/
cp2k.popt(main+0x1fffffffff523f30) [0x4000000000076d40]
[17] func:/lib/tls/libc.so.6.1(__libc_start_main-0x2bccc0)
[0x2000000000899c50]
[18] func:/home/users/eshamay/tmp/cp2k/exe/Linux-ia64-intel/
cp2k.popt(_start+0x1fffffffff520160) [0x4000000000076a80]
*** End of error message ***
6] func:/home/users/eshamay/tmp/cp2k/exe/Linux-ia64-intel/
cp2k.popt(main+0x1fffffffff523f30) [0x4000000000076d40]
[17] func:/lib/tls/libc.so.6.1(__libc_start_main-0x2bccc0)
[0x2000000000899c50]
[18] func:/home/users/eshamay/tmp/cp2k/exe/Linux-ia64-intel/
cp2k.popt(_start+0x1fffffffff520160) [0x4000000000076a80]
*** End of error message ***
6] func:/home/users/eshamay/tmp/cp2k/exe/Linux-ia64-intel/
cp2k.popt(main+0x1fffffffff523f30) [0x4000000000076d40]
[17] func:/lib/tls/libc.so.6.1(__libc_start_main-0x2bccc0)
[0x2000000000899c50]
[18] func:/home/users/eshamay/tmp/cp2k/exe/Linux-ia64-intel/
cp2k.popt(_start+0x1fffffffff520160) [0x4000000000076a80]
*** End of error message ***
mpirun noticed that job rank 1 with PID 14565 on node "localhost"
exited on signal 11.
So far all the help was right on track and I've finally been able to
get it to compile, but now I'm stuck at this near-immediate crash
after trying to run the program in parallel. Any further help would be
greatly appreciated.
~Eric
On May 28, 12:12 pm, akohlmey <akoh... at gmail.com> wrote:
> On May 28, 2:57 pm, Eric Shamay <eric.... at gmail.com> wrote:
>
> > Thank you for the help with the compiler. I installed a newer version
> > and overcame the previous error. Now I'm stuck with an error involving
> > libmkl_scalapack:
>
> > IPO link: can not find -lmkl_scalapack
> > ifort: error: problem during multi-file optimization compilation (code
> > 1)
>
> > Installing the latest version of Intel's mkl does not include
> > libmkl_scalapack, and so I'm left wondering where I can find that
> > particular library.
>
> eric,
> you have to either use intel's cluster mkl or compile
> BLACS/ScaLAPACK yourself.
>
> you can see my notes on how i compiled both packages for our group at:https://www.liniac.upenn.edu//wiki/tiki-index.php?page=scalapack+for+CMM
>
> you will have to adapt the configuration files for your MPI
> installation.
> when compiling BLACS/ScaLAPACK it is essential to verify your
> compilation
> with the corresponding testers. BLACS should pass completely, in
> ScaLAPACK
> you may get away with a few tests failing (minor). the success of the
> latter
> depends also a lot on the optimizations in the BLAS/LAPACK that is
> used
> with ScaLAPACK. i had the best successes with mkl.
> it is important not to overoptimize.
>
> hope this helps,
> axel.
>
> > Thanks,
> > ~Eric
>
> > On May 24, 11:54 am, "Nichols A. Romero" <naro... at gmail.com> wrote:
>
> > > 9.1.041 also works for me.
>
> > > On 5/24/07, Teodoro Laino <teodor... at gmail.com> wrote:
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