Dear Akbar,
The module mpi_siesta should be included in the library libmpi_f90.a. In
my opinion, the error message simply means your libmpi_f90.a is probably
not a good one. I noticed that you are using the libmpi_f90.a library
compiled with your local machine. I'm not sure if that's a good idea. So
my suggestions would be the following:
1) Use Siesta's own implementation of libmpi_f90.a, which means changing
the MPI_INTERFACE to simply "./libmpi_f90.a".
2) To compile the libmpi_f90.a library, you should assign the right path
to MPI_INCLUDE. So set MPI_INCLUDE to "your_mpi_directory/include" in
which the "mpi.h" file should exist.
3) Add -DMPI to FPPFLAGS. Do a full clean by "make clean", then compile
the code again.
Good luck,
Hui
akbar jahangiri wrote:
here is the file
On Fri, Feb 26, 2010 at 8:00 PM, akbar jahangiri <a.a.j.j...@gmail.com
<mailto:a.a.j.j...@gmail.com>> wrote:
Dear Friends
Thank you very much.
The problem is not solved completely i was able to compile SIESTA
in parallel mode but while running still the same output with too
many liens which are saying SERIAL MODE are there (as i checked on
the node of clusters which SIESTA was running ) that is true
;means SIESTA is working in serial mode . i am sending my last
arch.make file.
as far as you see there is no sign of -DMPI which my Friends
Andrey an Lucas mentioned.the reason is that when i add this
option to my arch.make file the compilation will give me another
error :
________________________________________________________________________________________________________
mpif90 -c -g -O2 `FoX/FoX-config --fcflags` -DMPI
-DFC_HAVE_FLUSH -DFC_HAVE_ABORT sys.F
fortcom: Error: sys.F, line 23: Error in opening the compiled
module file. Check INCLUDE paths. [MPI_SIESTA]
use mpi_siesta
----------^
fortcom: Error: sys.F, line 42: Error in opening the compiled
module file. Check INCLUDE paths. [MPI_SIESTA]
use mpi_siesta
----------^
fortcom: Error: sys.F, line 81: Error in opening the compiled
module file. Check INCLUDE paths. [MPI_SIESTA]
use mpi_siesta
----------^
compilation aborted for sys.F (code 1)
____________________________________________________________________________________________________________
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
can anyone help?
Thank you
best regards
Akbar
On Thu, Feb 25, 2010 at 8:28 PM, Zhen Huang <huan...@purdue.edu
<mailto:huan...@purdue.edu>> wrote:
that means your blacs is not included in your arch.make. find
where your blacs is and change the following in your arch.make.
BLACS_LIBS=/apps/rhel5/blacs/64/nemesis-gcc-4.4.0/lib/blacsF77init_MPI-LINUX-0.a
/apps/rhel5/blacs/64/nemesis-gcc-4.4.0/lib/blacs_MPI-LINUX-0.a
SCALAPACK_LIBS=/apps/rhel5/scalapack/64/gcc-4.4.0/lib/libscalapack.a
Best Regards
-------
Zhen (Alex) Huang
Ph.D. Student
Nanoscale Transport Research Group
Laboratory for Computational Methods in Emerging Technologies
Cooling Technologies Research Center
School of Mechanical Engineering
Purdue University
Tel: 765 237 9733
On Thu, Feb 25, 2010 at 9:13 AM, akbar jahangiri
<a.a.j.j...@gmail.com <mailto:a.a.j.j...@gmail.com>> wrote:
Dear Freinds
This is the error ..
______________________________________________________________________________________________________________
**********************************************************************************************************************************************************
dc_lapack.a `FoX/FoX-config --libs --wcml` -L
/opt/Libraries/scalapack-1.7.4/libscalapack.a -L
/opt/Libraries/BLACS/LIB/blacsF77init_MPI-LINUX-0.a -L
/opt/Libraries/BLACS/LIB/blacs_MPI-LINUX-0.a -L
/opt/Libraries/BLACS/LIB/blacsF77init_MPI-LINUX-0.a -L
/opt/Libraries/BLACS/LIB/blacsCinit_MPI-LINUX-0.a -llapack
-L /usr/lib64/ -lblas -L
/usr/lib/gcc/x86_64-redhat-linux/3.4.3/ -lg2c -DCDF
cdiag.o(.text+0x62a): In function `cdiag_':
: undefined reference to `blacs_gridinfo_'
cdiag.o(.text+0x64e): In function `cdiag_':
.......
......
.....
: undefined reference to `blacs_get_'
cdiag.o(.text+0x2b226): In function `cdiag_':
: undefined reference to `blacs_gridinit_'
rdiag.o(.text+0x50d): In function `rdiag_':
....
.....
....
rdiag.o(.text+0x22b7d): In function `rdiag_':
: undefined reference to `blacs_gridinit_'
make: *** [siesta] Error 1
__________________________________________________________________________________________________
******************************************************************************************************************************************
could you please Tell me what can i do?
thank you
Best regards
Akbar
On Thu, Feb 25, 2010 at 7:37 PM, akbar jahangiri
<a.a.j.j...@gmail.com <mailto:a.a.j.j...@gmail.com>> wrote:
Dear Zhen
i used MPI compiler,just i made FC=ifort as comment by
using # sign.
Thank you very much
Best regards
Akbar
On Thu, Feb 25, 2010 at 7:25 PM, Zhen Huang
<huan...@purdue.edu <mailto:huan...@purdue.edu>> wrote:
I saw you were using ifort to compile you should
use a mpi compiler. check
module avil mpi on your computer.
--
Zhen Huang
Ph.D. Student
Nanoscale Transport Research Group
School of Mechanical Engineering
Purdue University
Tel: 765 722 1113
Quoting akbar jahangiri <a.a.j.j...@gmail.com
<mailto:a.a.j.j...@gmail.com>>:
> Dear Zhen
>
> yes, i checked it before but it was not able to
find my libraries so i had
> to specified the location of libraries (which
seems is cause of problem).
>
> Thank you
> Best regards
> Akbar
>
> On Thu, Feb 25, 2010 at 6:39 PM, Zhen Huang
<huan...@purdue.edu <mailto:huan...@purdue.edu>>
wrote:
>
> > HI Akbar-
> >
> > check URDIR/configure --help. There is a mpi
enable choice. When you
> > configure the system you need to turn on mpi
choice.
> >
> > Best Regards
> > -------
> > Zhen (Alex) Huang
> > Ph.D. Student
> > Nanoscale Transport Research Group
> > Laboratory for Computational Methods in
Emerging Technologies
> > Cooling Technologies Research Center
> > School of Mechanical Engineering
> > Purdue University
> > Tel: 765 237 9733
> >
> >
> >
> > On Thu, Feb 25, 2010 at 1:47 AM, akbar jahangiri
> <a.a.j.j...@gmail.com
<mailto:a.a.j.j...@gmail.com>>wrote:
> >
> >> Dear Users
> >>
> >> I have Compile and run siesta in parallel
mode.but when i look at my
> >> <systemlable>.out file i see at the bigining
that written
> >>
> >> Siesta Version: siesta-2.0.2
> >> Architecture : x86_64-unknown-linux-gnu--Intel
> >> Compiler flags: ifort -g
> >> SERIAL version
> >>
> >> * Running in serial mode
> >> >> Start of run: 25-FEB-2010 11:59:07
> >> Siesta Version: siesta-2.0.2
> >> Architecture : x86_64-unknown-linux-gnu--Intel
> >> Compiler flags: ifort -g
> >> SERIAL version
> >>
> >> * Running in serial mode
> >> >> Start of run: 25-FEB-2010 11:59:07
> >> Siesta Version: siesta-2.0.2
> >> Architecture : x86_64-unknown-linux-gnu--Intel
> >> Compiler flags: ifort -g
> >> SERIAL version
> >>
> >> * Running in serial mode
> >> >> Start of run: 25-FEB-2010 11:59:07
> >> Siesta Version: siesta-2.0.2
> >> Architecture : x86_64-unknown-linux-gnu--Intel
> >> Compiler flags: ifort -g
> >> SERIAL version
> >>
> >> * Running in serial mode
> >> >> Start of run: 25-FEB-2010 11:59:07
> >>
> >>
***********************
> >> * WELCOME TO
SIESTA *
> >>
***********************
> >>
> >>
***********************
> >> * WELCOME TO
SIESTA *
> >>
***********************
> >>
> >> reinit: Reading from standard input
> >>
> >> reinit: Reading from standard input
> >>
> >>
***********************
> >> * WELCOME TO
SIESTA *
> >>
***********************
> >>
> >> reinit: Reading from standard input
> >>
> >>
***********************
> >> * WELCOME TO
SIESTA *
> >>
***********************
> >> ************************** Dump of input data
file
> >> ****************************
> >> "../../parallelversion/parallel/h2o.out" 1227L,
> >> 49665C
> >> 1,1 Top
> >>
> >> my question is that whether i compiled Siesta
for running in parralel
> mode
> >> or not since it is say (out put file ) "
running in serial mode " for
> four
> >> times.
> >>
> >> is that because i used 4 prosesor to run this
job?
> >>
> >> if it is so why it is not writting paralel mode ?
> >>
> >>
> >> Thank you
> >> Best Regards
> >> Akbar
> >>
> >>
> >>
> >>
> >>
> >
>
