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Today's Topics:
1. Scyld Beowulf and openmpi (Rima Chaudhuri)
2. Re: Scyld Beowulf and openmpi (Ralph Castain)
3. Problems installing in Cygwin - Problem with GCC 3.4.4
(Gustavo Seabra)
4. Re: MPI + Mixed language coding(Fortran90 + C++) (Jeff Squyres)
5. Re: Problems installing in Cygwin - Problem with GCC 3.4.4
(Jeff Squyres)
----------------------------------------------------------------------
Message: 1
Date: Mon, 3 Nov 2008 11:30:01 -0600
From: "Rima Chaudhuri" <rima.chaudh...@gmail.com>
Subject: [OMPI users] Scyld Beowulf and openmpi
To: us...@open-mpi.org
Message-ID:
<7503b17d0811030930i13acb974kc627983a1d481...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hello!
I am a new user of openmpi -- I've installed openmpi 1.2.6 for our
x86_64 linux scyld beowulf cluster inorder to make it run with
amber10
MD simulation package.
The nodes can see the home directory i.e. a bpsh to the nodes works
fine and lists all the files in the home directory where I have
both
openmpi and amber10 installed.
However if I try to run:
$MPI_HOME/bin/mpirun -no_local=1 -np 4 $AMBERHOME/exe/
sander.MPI ........
I get the following error:
[0,0,0] ORTE_ERROR_LOG: Not available in file ras_bjs.c at line 247
--------------------------------------------------------------------------
Failed to find the following executable:
Host: helios.structure.uic.edu
Executable: -o
Cannot continue.
--------------------------------------------------------------------------
[helios.structure.uic.edu:23611] [0,0,0] ORTE_ERROR_LOG: Not
found in
file rmgr_urm.c at line 462
[helios.structure.uic.edu:23611] mpirun: spawn failed with
errno=-13
any cues?
--
-Rima
------------------------------
Message: 2
Date: Mon, 3 Nov 2008 12:08:36 -0700
From: Ralph Castain <r...@lanl.gov>
Subject: Re: [OMPI users] Scyld Beowulf and openmpi
To: Open MPI Users <us...@open-mpi.org>
Message-ID: <91044a7e-ada5-4b94-aa11-b3c1d9843...@lanl.gov>
Content-Type: text/plain; charset=US-ASCII; format=flowed;
delsp=yes
For starters, there is no "-no_local" option to mpirun. You might
want
to look at mpirun --help, or man mpirun.
I suspect the option you wanted was --nolocal. Note that --nolocal
does not take an argument.
Mpirun is confused by the incorrect option and looking for an
incorrectly named executable.
Ralph
On Nov 3, 2008, at 10:30 AM, Rima Chaudhuri wrote:
Hello!
I am a new user of openmpi -- I've installed openmpi 1.2.6 for our
x86_64 linux scyld beowulf cluster inorder to make it run with
amber10
MD simulation package.
The nodes can see the home directory i.e. a bpsh to the nodes
works
fine and lists all the files in the home directory where I have
both
openmpi and amber10 installed.
However if I try to run:
$MPI_HOME/bin/mpirun -no_local=1 -np 4 $AMBERHOME/exe/
sander.MPI ........
I get the following error:
[0,0,0] ORTE_ERROR_LOG: Not available in file ras_bjs.c at line
247
--------------------------------------------------------------------------
Failed to find the following executable:
Host: helios.structure.uic.edu
Executable: -o
Cannot continue.
--------------------------------------------------------------------------
[helios.structure.uic.edu:23611] [0,0,0] ORTE_ERROR_LOG: Not found
in
file rmgr_urm.c at line 462
[helios.structure.uic.edu:23611] mpirun: spawn failed with
errno=-13
any cues?
--
-Rima
_______________________________________________
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
------------------------------
Message: 3
Date: Mon, 3 Nov 2008 14:53:55 -0500
From: "Gustavo Seabra" <gustavo.sea...@gmail.com>
Subject: [OMPI users] Problems installing in Cygwin - Problem with
GCC
3.4.4
To: "Open MPI Users" <us...@open-mpi.org>
Message-ID:
<f79359b60811031153l5591e0f8j49a7e4d9fb02e...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi everyone,
Here's a "progress report"... more questions in the end :-)
Finally, I was *almost* able to compile OpenMPI in Cygwin using the
following configure command:
./configure --prefix=/home/seabra/local/openmpi-1.3b1 \
--with-mpi-param_check=always --with-threads=posix \
--enable-mpi-threads --disable-io-romio \
--enable-mca-no-
build=memory_mallopt,maffinity,paffinity \
--enable-contrib-no-build=vt \
FC=g95 'FFLAGS=-O0 -fno-second-underscore' CXX=g++
I then had a very weird error during compilation of
ompi/tools/ompi_info/params.cc. (See below).
The lines causing the compilation errors are:
vector.tcc:307: const size_type __len = __old_size +
std::max(__old_size, __n);
vector.tcc:384: const size_type __len = __old_size +
std::max(__old_size, __n);
stl_bvector.h:522: const size_type __len = size() +
std::max(size(), __n);
stl_bvector.h:823: const size_type __len = size() +
std::max(size(), __n);
(Notice that those are from the standard gcc libraries.)
After googling it for a while, I could find that this error is
caused
because, at come point, the source code being compiled redefined
the
"max" function with a macro, g++ cannot recognize the "std::max"
that
happens in those lines and only "sees" a (...), thus printing that
cryptic complaint.
I looked in some places in the OpenMPI code, but I couldn't find
"max" being redefined anywhere, but I may be looking in the wrong
places. Anyways, the only way of found of compiling OpenMPI was a
very
ugly hack: I have to go into those files and remove the "std::"
before
the "max". With that, it all compiled cleanly.
I did try running the tests in the 'tests' directory (with 'make
check'), and I didn't get any alarming message, except that in some
cases (class, threads, peruse) it printed "All 0 tests passed". I
got
and "All (n) tests passed" (n>0) for asm and datatype.
Can anybody comment on the meaning of those test results? Should
I be
alarmed with the "All 0 tests passed" messages?
Finally, in the absence of big red flags (that I noticed), I went
ahead and tried to compile my program. However, as soon as
compilation
starts, I get the following:
/local/openmpi/openmpi-1.3b1/bin/mpif90 -c -O3 -fno-second-
underscore
-ffree-form -o constants.o _constants.f
--------------------------------------------------------------------------
Unfortunately, this installation of Open MPI was not compiled with
Fortran 90 support. As such, the mpif90 compiler is non-
functional.
--------------------------------------------------------------------------
make[1]: *** [constants.o] Error 1
make[1]: Leaving directory `/home/seabra/local/amber11/src/sander'
make: *** [parallel] Error 2
Notice that I compiled OpenMPI with g95, so there *should* be
Fortran95 support... Any ideas on what could be going wrong?
Thank you very much,
Gustavo.
======================================
Error in the compilation of params.cc
======================================
$ g++ -DHAVE_CONFIG_H -I. -I../../../opal/include
-I../../../orte/include -I../../../ompi/include
-I../../../opal/mca/paffinity/linux/plpa/src/libplpa
-DOMPI_CONFIGURE_USER="\"seabra\"" -
DOMPI_CONFIGURE_HOST="\"ACS02\""
-DOMPI_CONFIGURE_DATE="\"Sat Nov 1 20:44:32 EDT 2008\""
-DOMPI_BUILD_USER="\"$USER\"" -DOMPI_BUILD_HOST="\"`hostname`\""
-DOMPI_BUILD_DATE="\"`date`\"" -DOMPI_BUILD_CFLAGS="\"-O3 -DNDEBUG
-finline-functions -fno-strict-aliasing \""
-DOMPI_BUILD_CPPFLAGS="\"-I../../.. -D_REENTRANT\""
-DOMPI_BUILD_CXXFLAGS="\"-O3 -DNDEBUG -finline-functions \""
-DOMPI_BUILD_CXXCPPFLAGS="\"-I../../.. -D_REENTRANT\""
-DOMPI_BUILD_FFLAGS="\"-O0 -fno-second-underscore\""
-DOMPI_BUILD_FCFLAGS="\"\"" -DOMPI_BUILD_LDFLAGS="\"-export-dynamic
\"" -DOMPI_BUILD_LIBS="\"-lutil \""
-DOMPI_CC_ABSOLUTE="\"/usr/bin/gcc\""
-DOMPI_CXX_ABSOLUTE="\"/usr/bin/g++\""
-DOMPI_F77_ABSOLUTE="\"/usr/bin/g77\""
-DOMPI_F90_ABSOLUTE="\"/usr/local/bin/g95\""
-DOMPI_F90_BUILD_SIZE="\"small\"" -I../../.. -D_REENTRANT -O3
-DNDEBUG -finline-functions -MT param.o -MD -MP -MF $depbase.Tpo
-c
-o param.o param.cc
In file included from /usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c+
+/
vector:72,
from ../../../ompi/tools/ompi_info/ompi_info.h:24,
from param.cc:43:
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_bvector.h:
In
member function `void std::vector<bool,
_Alloc>::_M_insert_range(std::_Bit_iterator, _ForwardIterator,
_ForwardIterator, std::forward_iterator_tag)':
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_bvector.h:
522:
error: expected unqualified-id before '(' token
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_bvector.h:
In
member function `void std::vector<bool,
_Alloc>::_M_fill_insert(std::_Bit_iterator, size_t, bool)':
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/stl_bvector.h:
823:
error: expected unqualified-id before '(' token
In file included from /usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c+
+/
vector:75,
from ../../../ompi/tools/ompi_info/ompi_info.h:24,
from param.cc:43:
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/vector.tcc: In
member function `void std::vector<_Tp,
_Alloc>::_M_fill_insert(__gnu_cxx::__normal_iterator<typename
_Alloc::pointer, std::vector<_Tp, _Alloc> >, size_t, const _Tp&)':
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/vector.tcc:307:
error: expected unqualified-id before '(' token
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/vector.tcc: In
member function `void std::vector<_Tp,
_Alloc>::_M_range_insert(__gnu_cxx::__normal_iterator<typename
_Alloc::pointer, std::vector<_Tp, _Alloc> >, _ForwardIterator,
_ForwardIterator, std::forward_iterator_tag)':
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/vector.tcc:384:
error: expected unqualified-id before '(' token
--
Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
------------------------------
Message: 4
Date: Mon, 3 Nov 2008 14:54:25 -0500
From: Jeff Squyres <jsquy...@cisco.com>
Subject: Re: [OMPI users] MPI + Mixed language coding(Fortran90 +
C+
+)
To: Open MPI Users <us...@open-mpi.org>
Message-ID: <45698801-0857-466f-a19d-c529f72d4...@cisco.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed;
delsp=yes
Can you replicate the scenario in smaller / different cases?
- write a sample plugin in C instead of C++
- write a non-MPI Fortran application that loads your C++
application
- ...?
In short, *MPI* shouldn't be interfering with Fortran/C++ common
blocks. Try taking MPI out of the picture and see if that makes
the
problem go away.
Those are pretty much shots in the dark, but I don't know where to
go,
either -- try random things until you find what you want.
On Nov 3, 2008, at 3:51 AM, Rajesh Ramaya wrote:
Helllo Jeff, Gustavo, Mi
Thank for the advice. I am familiar with the difference in the
compiler code generation for C, C++ & FORTRAN. I even tried to
look
at some of the common block symbols. The name of the symbol
remains
the same. The only difference that I observe is in FORTRAN
compiled
*.o 0000000000515bc0 B aux7loc_ and the C++ compiled code U
aux7loc_ the memory is not allocated as it has been declared as
extern in C++. When the executable loads the shared library it
finds
all the undefined symbols. Atleast if it did not manage to find a
single symbol it prints undefined symbol error.
I am completely stuck up and do not know how to continue further.
Thanks,
Rajesh
From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org
]
On Behalf Of Mi Yan
Sent: samedi 1 novembre 2008 23:26
To: Open MPI Users
Cc: 'Open MPI Users'; users-boun...@open-mpi.org
Subject: Re: [OMPI users] MPI + Mixed language coding(Fortran90
+ C
++)
So your tests show:
1. "Shared library in FORTRAN + MPI executable in FORTRAN" works.
2. "Shared library in C++ + MPI executable in FORTRAN " does not
work.
It seems to me that the symbols in C library are not really
recognized by FORTRAN executable as you thought. What compilers
did
yo use to built OpenMPI?
Different compiler has different convention to handle symbols.
E.g.
if there is a variable "var_foo" in your FORTRAN code, some FORTRN
compiler will save "var_foo_" in the object file by default; if
you
want to access "var_foo" in C code, you actually need to refer
"var_foo_" in C code. If you define "var_foo" in a module in the
FORTAN compiler, some FORTRAN compiler may append the module
name to
"var_foo".
So I suggest to check the symbols in the object files generated by
your FORTAN and C compiler to see the difference.
Mi
<image001.gif>"Rajesh Ramaya" <rajesh.ram...@e-xstream.com>
"Rajesh Ramaya" <rajesh.ram...@e-xstream.com>
Sent by: users-boun...@open-mpi.org
10/31/2008 03:07 PM
Please respond to
Open MPI Users <us...@open-mpi.org>
<image002.gif>
To
<image003.gif>
"'Open MPI Users'" <us...@open-mpi.org>, "'Jeff Squyres'" <jsquy...@cisco.com
<image002.gif>
cc
<image003.gif>
<image002.gif>
Subject
<image003.gif>
Re: [OMPI users] MPI + Mixed language coding(Fortran90 + C++)
<image003.gif>
<image003.gif>
Hello Jeff Squyres,
Thank you very much for the immediate reply. I am able to
successfully
access the data from the common block but the values are zero.
In my
algorithm I even update a common block but the update made by the
shared
library is not taken in to account by the executable. Can you
please
be very
specific how to make the parallel algorithm aware of the data?
Actually I am
not writing any MPI code inside? It's the executable (third party
software)
who does that part. All that I am doing is to compile my code with
MPI c
compiler and add it in the LD_LIBIRARY_PATH.
In fact I did a simple test by creating a shared library using a
FORTRAN
code and the update made to the common block is taken in to
account
by the
executable. Is there any flag or pragma that need to be activated
for mixed
language MPI?
Thank you once again for the reply.
Rajesh
-----Original Message-----
From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org
]
On
Behalf Of Jeff Squyres
Sent: vendredi 31 octobre 2008 18:53
To: Open MPI Users
Subject: Re: [OMPI users] MPI + Mixed language coding(Fortran90
+ C
++)
On Oct 31, 2008, at 11:57 AM, Rajesh Ramaya wrote:
I am completely new to MPI. I have a basic question concerning
MPI and mixed language coding. I hope any of you could help me
out.
Is it possible to access FORTRAN common blocks in C++ in a MPI
compiled code. It works without MPI but as soon I switch to MPI
the
access of common block does not work anymore.
I have a Linux MPI executable which loads a shared library at
runtime and resolves all undefined symbols etc The shared
library
is written in C++ and the MPI executable in written in FORTRAN.
Some
of the input that the shared library looking for are in the
Fortran
common blocks. As I access those common blocks during runtime the
values are not initialized. I would like to know if what I am
doing is possible ?I hope that my problem is clear......
Generally, MPI should not get in the way of sharing common blocks
between Fortran and C/C++. Indeed, in Open MPI itself, we share a
few
common blocks between Fortran and the main C Open MPI
implementation.
What is the exact symptom that you are seeing? Is the application
failing to resolve symbols at run-time, possibly indicating that
something hasn't instantiated a common block? Or are you able to
successfully access the data from the common block, but it doesn't
have the values you expect (e.g., perhaps you're seeing all
zeros)?
If the former, you might want to check your build procedure. You
*should* be able to simply replace your C++ / F90 compilers with
mpicxx and mpif90, respectively, and be able to build an MPI
version
of your app. If the latter, you might need to make your parallel
algorithm aware of what data is available in which MPI process --
perhaps not all the data is filled in on each MPI process...?
--
Jeff Squyres
Cisco Systems
_______________________________________________
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_______________________________________________
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--
Jeff Squyres
Cisco Systems
------------------------------
Message: 5
Date: Mon, 3 Nov 2008 15:04:47 -0500
From: Jeff Squyres <jsquy...@cisco.com>
Subject: Re: [OMPI users] Problems installing in Cygwin - Problem
with
GCC 3.4.4
To: Open MPI Users <us...@open-mpi.org>
Message-ID: <8e364b51-6726-4533-ade2-aea266380...@cisco.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed;
delsp=yes
On Nov 3, 2008, at 2:53 PM, Gustavo Seabra wrote:
Finally, I was *almost* able to compile OpenMPI in Cygwin using
the
following configure command:
./configure --prefix=/home/seabra/local/openmpi-1.3b1 \
--with-mpi-param_check=always --with-threads=posix \
--enable-mpi-threads --disable-io-romio \
--enable-mca-no-
build=memory_mallopt,maffinity,paffinity \
--enable-contrib-no-build=vt \
FC=g95 'FFLAGS=-O0 -fno-second-underscore' CXX=g++
For your fortran issue, the Fortran 90 interface needs the
Fortran 77
interface. So you need to supply an F77 as well (the output from
configure should indicate that the F90 interface was disabled
because
the F77 interface was disabled).
I then had a very weird error during compilation of
ompi/tools/ompi_info/params.cc. (See below).
The lines causing the compilation errors are:
vector.tcc:307: const size_type __len = __old_size +
std::max(__old_size, __n);
vector.tcc:384: const size_type __len = __old_size +
std::max(__old_size, __n);
stl_bvector.h:522: const size_type __len = size() +
std::max(size(), __n);
stl_bvector.h:823: const size_type __len = size() +
std::max(size(), __n);
(Notice that those are from the standard gcc libraries.)
After googling it for a while, I could find that this error is
caused
because, at come point, the source code being compiled redefined
the
"max" function with a macro, g++ cannot recognize the "std::max"
that
happens in those lines and only "sees" a (...), thus printing that
cryptic complaint.
I looked in some places in the OpenMPI code, but I couldn't find
"max" being redefined anywhere, but I may be looking in the wrong
places. Anyways, the only way of found of compiling OpenMPI was a
very
ugly hack: I have to go into those files and remove the "std::"
before
the "max". With that, it all compiled cleanly.
I'm not sure I follow -- I don't see anywhere in OMPI where we use
std::max. What areas did you find that you needed to change?
I did try running the tests in the 'tests' directory (with 'make
check'), and I didn't get any alarming message, except that in
some
cases (class, threads, peruse) it printed "All 0 tests passed". I
got
and "All (n) tests passed" (n>0) for asm and datatype.
Can anybody comment on the meaning of those test results? Should I
be
alarmed with the "All 0 tests passed" messages?
No. We don't really maintain the "make check" stuff too well.
--
Jeff Squyres
Cisco Systems
------------------------------
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End of users Digest, Vol 1055, Issue 2
**************************************
