problem compiling PETSC on MacOS Leopard
unsigned char *,
unsigned);
void setprogname(const char *);
int sradixsort(const unsigned char **, int, const unsigned char *,
unsigned);
void sranddev(void);
void srandomdev(void);
void *reallocf(void *, size_t);
long long
strtoq(const char *, char **, int);
unsigned long long
strtouq(const char *, char **, int);
extern char *suboptarg;
void *valloc(size_t);
# 3 conftest.c 2
Popping language C
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=
=
=
=
=
=
=
TEST checkCxxCompiler from config.setCompilers(/Users/bknaepen/Unix/
petsc-2.3.3-p8/python/BuildSystem/config/setCompilers.py:541)
TESTING: checkCxxCompiler from config.setCompilers(python/BuildSystem/
config/setCompilers.py:541)
Locate a functional Cxx compiler
=
=
=
=
=
=
=
=
TEST checkFortranCompiler from config.setCompilers(/Users/bknaepen/
Unix/petsc-2.3.3-p8/python/BuildSystem/config/setCompilers.py:708)
TESTING: checkFortranCompiler from config.setCompilers(python/
BuildSystem/config/setCompilers.py:708)
Locate a functional Fortran compiler
Checking for program /opt/intel/fc/10.0.020/bin/mpif90...not found
Checking for program /usr/X11R6/bin/mpif90...not found
Checking for program /opt/toolworks/totalview.8.3.0-0/bin/mpif90...not
found
Checking for program /Users/bknaepen/Unix/mpich2-106/bin/mpif90...found
Defined make macro FC to mpif90
Pushing language FC
sh: mpif90 -c -o conftest.o conftest.F
Executing: mpif90 -c -o conftest.o conftest.F
sh:
Possible ERROR while running compiler: ret = 256
error message = {ifort: error #10106: Fatal error in /opt/intel/fc/
10.0.020/bin/fpp, terminated by segmentation violation
}
Source:
program main
end
Popping language FC
Error testing Fortran compiler: Cannot compile FC with mpicc.
MPI installation mpif90 is likely incorrect.
Use --with-mpi-dir to indicate an alternate MPI.
*
UNABLE to CONFIGURE with GIVEN OPTIONS(see configure.log
for details):
---
Fortran compiler you provided with --with-fc=mpif90 does not work
*
File ./config/configure.py, line 190, in petsc_configure
framework.configure(out = sys.stdout)
File /Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/
framework.py, line 878, in configure
child.configure()
File /Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/
setCompilers.py, line 1267, in configure
self.executeTest(self.checkFortranCompiler)
File /Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/
base.py, line 93, in executeTest
return apply(test, args,kargs)
File /Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/
setCompilers.py, line 714, in checkFortranCompiler
for compiler in self.generateFortranCompilerGuesses():
File /Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/
setCompilers.py, line 631, in generateFortranCompilerGuesses
raise RuntimeError('Fortran compiler you provided with --with-
fc='+self.framework.argDB['with-fc']+' does not work')
-- next part --
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problem compiling PETSC on MacOS Leopard
Please direct these problems to petsc-maint instead of petsc-users.
From the log file
Checking for program /Users/bknaepen/Unix/mpich2-106/bin/mpif90...found
Defined make macro FC to mpif90
Pushing language FC
sh: mpif90 -c -o conftest.o conftest.F
Executing: mpif90 -c -o conftest.o conftest.F
sh:
Possible ERROR while running compiler: ret =3D 256
error message =3D {ifort: error #10106: Fatal error in /opt/intel/fc/=20
10.0.020/bin/fpp, terminated by segmentation violation
}
Source:
program main
end
So the mpif90 is crashing on a simple Fortran program with nothing
in it. Can you try compiling exactly as above from the command line?
Barry
On Sun, 18 Nov 2007, Bernard Knaepen wrote:
Hello,
I would like to compile PETSC on Leopard but I am encountering a problem
during configuration. The scripts stops with:
dolfin:petsc-2.3.3-p8 bknaepen$ ./config/configure.py --with-cc=mpicc
--with-fc=mpif90 --with-cxx=mpicxx
=
Configuring PETSc to compile on your system
=
TESTING: checkFortranCompiler from
config.setCompilers(python/BuildSystem/config/setCompilers.py:708)
*
UNABLE to CONFIGURE with GIVEN OPTIONS(see configure.log for
details):
---
Fortran compiler you provided with --with-fc=mpif90 does not work
*
My MPI installation is mpich2 1.0.6p1 and I have the latest ifort compiler
installed (10.0.20). I have test mpif90 and it is working ok. I copy below
the configure.log file.
Any help would be appreciated, thanks,
Bernard.
Pushing language C
Popping language C
Pushing language Cxx
Popping language Cxx
Pushing language FC
Popping language FC
sh: /bin/sh
/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/packages/config.guess
Executing: /bin/sh
/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/packages/config.guess
sh: i686-apple-darwin9.1.0
sh: /bin/sh
/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/packages/config.sub
i686-apple-darwin9.1.0
Executing: /bin/sh
/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/packages/config.sub
i686-apple-darwin9.1.0
sh: i686-apple-darwin9.1.0
Starting Configure Run at Sun Nov 18 10:29:29 2007
Configure Options: --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpicxx
--with-shared=0 --configModules=PETSc.Configure
--optionsModule=PETSc.compilerOptions
Working directory: /Users/bknaepen/Unix/petsc-2.3.3-p8
Python version:
2.5.1 (r251:54863, Oct 5 2007, 21:08:09)
[GCC 4.0.1 (Apple Inc. build 5465)]
Pushing language C
Popping language C
Pushing language Cxx
Popping language Cxx
Pushing language FC
Popping language FC
TEST configureExternalPackagesDir from
config.framework(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/framework.py:807)
TESTING: configureExternalPackagesDir from
config.framework(python/BuildSystem/config/framework.py:807)
TEST configureLibrary from
PETSc.packages.PVODE(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/packages/PVODE.py:10)
TESTING: configureLibrary from
PETSc.packages.PVODE(python/PETSc/packages/PVODE.py:10)
Find a PVODE installation and check if it can work with PETSc
TEST configureLibrary from
PETSc.packages.NetCDF(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/PETSc/packages/NetCDF.py:10)
TESTING: configureLibrary from
PETSc.packages.NetCDF(python/PETSc/packages/NetCDF.py:10)
Find a NetCDF installation and check if it can work with PETSc
TEST configureMercurial from
config.sourceControl(/Users/bknaepen/Unix/petsc-2.3.3-p8/python/BuildSystem/config/sourceControl.py:23)
TESTING: configureMercurial from
config.sourceControl(python/BuildSystem/config/sourceControl.py:23)
Find the Mercurial executable
Checking for program
problem compiling PETSC on MacOS Leopard
Executing: mpif90 -c -o conftest.o conftest.F
sh:
Possible ERROR while running compiler: ret = 256
error message = {ifort: error #10106: Fatal error in
/opt/intel/fc/10.0.020/bin/fpp, terminated by segmentation violation
ifort is giving SEGV - hence configure failed. There must be some
compatibility issue with ifort and Leopard.
Satish
On Sun, 18 Nov 2007, Bernard Knaepen wrote:
Hello,
I would like to compile PETSC on Leopard but I am encountering a problem
during configuration. The scripts stops with:
dolfin:petsc-2.3.3-p8 bknaepen$ ./config/configure.py --with-cc=mpicc
--with-fc=mpif90 --with-cxx=mpicxx
Parallel ISCreateGeneral()
Hi all, Just wanted to know if the the length of the index set for a call to ISCreateGeneral() in a parallel code, is a global length, or the length of the local elements on each process? Thanks, Tim. -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax)
Parallel ISCreateGeneral()
IS are not really parallel, so all the lengths, etc. only refer to local things. Matt On Nov 18, 2007 11:22 AM, Tim Stitt timothy.stitt at ichec.ie wrote: Hi all, Just wanted to know if the the length of the index set for a call to ISCreateGeneral() in a parallel code, is a global length, or the length of the local elements on each process? Thanks, Tim. -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
Parallel ISCreateGeneral()
On Nov 18, 2007 11:34 AM, Tim Stitt timothy.stitt at ichec.ie wrote: OK..so I should be using the aggregate length returned by MatGetOwnershipRange() routine? If you are using it to permute a Mat, yes. Matt Thanks Matt for you help. Matthew Knepley wrote: IS are not really parallel, so all the lengths, etc. only refer to local things. Matt On Nov 18, 2007 11:22 AM, Tim Stitt timothy.stitt at ichec.ie wrote: Hi all, Just wanted to know if the the length of the index set for a call to ISCreateGeneral() in a parallel code, is a global length, or the length of the local elements on each process? Thanks, Tim. -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
Parallel ISCreateGeneral()
Matt, It is in setup for MatLUFactorSymbolic() and MatLUFactorNumeric() calls which require index sets. I have distributed my rows across the processes and now just a bit confused about the arguments to the ISCreateGeneral() routine to set up the IS sets used by the Factor routines in parallel. So my basic question is what in general is the length and integers that get passed to ISCreateGeneral() when doing this type of calculation in parallel? Are they local index values (0..#rows on process-1) or do they refer to the distributed indices of the global matrix? Tim. Matthew Knepley wrote: On Nov 18, 2007 11:34 AM, Tim Stitt timothy.stitt at ichec.ie wrote: OK..so I should be using the aggregate length returned by MatGetOwnershipRange() routine? If you are using it to permute a Mat, yes. Matt Thanks Matt for you help. Matthew Knepley wrote: IS are not really parallel, so all the lengths, etc. only refer to local things. Matt On Nov 18, 2007 11:22 AM, Tim Stitt timothy.stitt at ichec.ie wrote: Hi all, Just wanted to know if the the length of the index set for a call to ISCreateGeneral() in a parallel code, is a global length, or the length of the local elements on each process? Thanks, Tim. -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax)
Parallel ISCreateGeneral()
On Nov 18, 2007 11:52 AM, Tim Stitt timothy.stitt at ichec.ie wrote: Matt, It is in setup for MatLUFactorSymbolic() and MatLUFactorNumeric() calls which require index sets. I have distributed my rows across the processes and now just a bit confused about the arguments to the ISCreateGeneral() routine to set up the IS sets used by the Factor routines in parallel. So my basic question is what in general is the length and integers that get passed to ISCreateGeneral() when doing this type of calculation in parallel? Are they local index values (0..#rows on process-1) or do they refer to the distributed indices of the global matrix? To be consistent, these would be local sizes and global numberings. However, I am not sure why you would be doing this. I do not believe any of the parallel LU packages accept an ordering from the user (they calculate their own), and I would really only use them from a KSP (or PC at the least). Matt Tim. Matthew Knepley wrote: On Nov 18, 2007 11:34 AM, Tim Stitt timothy.stitt at ichec.ie wrote: OK..so I should be using the aggregate length returned by MatGetOwnershipRange() routine? If you are using it to permute a Mat, yes. Matt Thanks Matt for you help. Matthew Knepley wrote: IS are not really parallel, so all the lengths, etc. only refer to local things. Matt On Nov 18, 2007 11:22 AM, Tim Stitt timothy.stitt at ichec.ie wrote: Hi all, Just wanted to know if the the length of the index set for a call to ISCreateGeneral() in a parallel code, is a global length, or the length of the local elements on each process? Thanks, Tim. -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
Parallel ISCreateGeneral()
Oh...ok I am now officially confused. I have developed a serial code for getting the first k rows of an inverted sparse matrix..thanks to PETSC users/developers help this past week. In that code I was calling MatLUFactorSymbolic() and MatLUFactorNumeric() to factor the sparse matrix and then calling MatSolve for each of the first k columns in the identity matrix as the RHS. I then varied the matrix type from the command line to test MUMPS, SUPERLU etc. for the best performance. Now I just want to translate the code into a parallel version...so I now assemble rows in a distributed fashion and now working on translating the MatLUFactorSymbolic() and MatLUFactorNumeric() calls which require index sets...hence my original question. Are you saying that I now shouldn't be calling those routines? Tim. Matthew Knepley wrote: On Nov 18, 2007 11:52 AM, Tim Stitt timothy.stitt at ichec.ie wrote: Matt, It is in setup for MatLUFactorSymbolic() and MatLUFactorNumeric() calls which require index sets. I have distributed my rows across the processes and now just a bit confused about the arguments to the ISCreateGeneral() routine to set up the IS sets used by the Factor routines in parallel. So my basic question is what in general is the length and integers that get passed to ISCreateGeneral() when doing this type of calculation in parallel? Are they local index values (0..#rows on process-1) or do they refer to the distributed indices of the global matrix? To be consistent, these would be local sizes and global numberings. However, I am not sure why you would be doing this. I do not believe any of the parallel LU packages accept an ordering from the user (they calculate their own), and I would really only use them from a KSP (or PC at the least). Matt Tim. Matthew Knepley wrote: On Nov 18, 2007 11:34 AM, Tim Stitt timothy.stitt at ichec.ie wrote: OK..so I should be using the aggregate length returned by MatGetOwnershipRange() routine? If you are using it to permute a Mat, yes. Matt Thanks Matt for you help. Matthew Knepley wrote: IS are not really parallel, so all the lengths, etc. only refer to local things. Matt On Nov 18, 2007 11:22 AM, Tim Stitt timothy.stitt at ichec.ie wrote: Hi all, Just wanted to know if the the length of the index set for a call to ISCreateGeneral() in a parallel code, is a global length, or the length of the local elements on each process? Thanks, Tim. -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax) -- Dr. Timothy Stitt timothy_dot_stitt_at_ichec.ie HPC Application Consultant - ICHEC (www.ichec.ie) Dublin Institute for Advanced Studies 5 Merrion Square - Dublin 2 - Ireland +353-1-6621333 (tel) / +353-1-6621477 (fax)
Dual core performance estimate
Hi, someone was talking abt core 2 duo performance on os x in some previous email. it seems that due to memory issues, it's not possible to get 2x the performance. there's also some mention of amd vs intel dual core. for computation using PETSc, is there any reason to buy one instead of the other? Also, supposed I use winxp + mpich2 + PETSc on a dual core, what sort of performance increase can we expect as compared to PETSc + nompi on the same machine? or is that too difficult an answer to give since there are too many factors? thank you regards -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20071118/4fbf2f74/attachment.htm
Dual core performance estimate
Hi Ben, You're asking a question that is very specific to the program you're running. I think the general consensus on this list has been that for the more common uses of PETSc, getting dual-cores will not speed up your performance as much as dual-processors. For OS X, dual-cores are pretty much the baseline now, so I wouldn't worry too much about it. ~A On Nov 18, 2007 3:34 PM, Ben Tay zonexo at gmail.com wrote: Hi, someone was talking abt core 2 duo performance on os x in some previous email. it seems that due to memory issues, it's not possible to get 2x the performance. there's also some mention of amd vs intel dual core. for computation using PETSc, is there any reason to buy one instead of the other? Also, supposed I use winxp + mpich2 + PETSc on a dual core, what sort of performance increase can we expect as compared to PETSc + nompi on the same machine? or is that too difficult an answer to give since there are too many factors? thank you regards
Dual core performance estimate
I asked the original question, and I have a follow up. Like it or not, multi-core CPUs have been thrust upon us by the manufacturers and many of us are more likely to have access to a shared memory, multi core/multi processor machine, than a properly built cluster with MPI in mind. So, two questions in this direction: 1. How feasible would it be to implement OpenMP in PETSc so that multi core CPUs could be properly used? 2. Even if we are building a cluster, it looks like AMD/Intel are thrusting multi core up on is. To that end, what is the feasibility of merging MPI and OpenMP so that between nodes, we use MPI, but within each node, OpenMP is used to take advantage of the multiple cores. -gideon On Nov 18, 2007, at 3:53 PM, Aron Ahmadia wrote: Hi Ben, You're asking a question that is very specific to the program you're running. I think the general consensus on this list has been that for the more common uses of PETSc, getting dual-cores will not speed up your performance as much as dual-processors. For OS X, dual-cores are pretty much the baseline now, so I wouldn't worry too much about it. ~A On Nov 18, 2007 3:34 PM, Ben Tay zonexo at gmail.com wrote: Hi, someone was talking abt core 2 duo performance on os x in some previous email. it seems that due to memory issues, it's not possible to get 2x the performance. there's also some mention of amd vs intel dual core. for computation using PETSc, is there any reason to buy one instead of the other? Also, supposed I use winxp + mpich2 + PETSc on a dual core, what sort of performance increase can we expect as compared to PETSc + nompi on the same machine? or is that too difficult an answer to give since there are too many factors? thank you regards -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20071118/8e49f4ba/attachment.htm
Dual core performance estimate
Gideon, On Sun, 18 Nov 2007, Gideon Simpson wrote: I asked the original question, and I have a follow up. Like it or not, multi-core CPUs have been thrust upon us by the manufacturers and many of us are more likely to have access to a shared memory, multi core/multi processor machine, than a properly built cluster with MPI in mind. So, two questions in this direction: 1. How feasible would it be to implement OpenMP in PETSc so that multi core CPUs could be properly used? 2. Even if we are building a cluster, it looks like AMD/Intel are thrusting multi core up on is. To that end, what is the feasibility of merging MPI and OpenMP so that between nodes, we use MPI, but within each node, OpenMP is used to take advantage of the multiple cores. -gideon Unfortunately using MPI+OpenMP on multi-core systems for the iterative solution of linear systems will not help AT ALL. Sparse matrix algorithms (like matrix-vector production, triangular solves) are memory bandwidth limited. The speed of the memory is not enough to support 2 (or more) processes both trying to pull sparse matrices from memory at the same time; the details of the parallelism are not the issue. Now it is possible that other parts of a PETSc code; like evaluating nonlinear functions, evaluating Jacobians and other stuff may NOT be memory bandwidth limited. Those parts of the code might benefit by using OpenMP on those pieces of the code, while only using the single thread on the linear solvers. That is, you would run PETSc with one MPI process per node, then in parts of your code you would use OpenMP loop level parallelism or OpenMP task parallelism. Barry On Nov 18, 2007, at 3:53 PM, Aron Ahmadia wrote: Hi Ben, You're asking a question that is very specific to the program you're running. I think the general consensus on this list has been that for the more common uses of PETSc, getting dual-cores will not speed up your performance as much as dual-processors. For OS X, dual-cores are pretty much the baseline now, so I wouldn't worry too much about it. ~A On Nov 18, 2007 3:34 PM, Ben Tay zonexo at gmail.com wrote: Hi, someone was talking abt core 2 duo performance on os x in some previous email. it seems that due to memory issues, it's not possible to get 2x the performance. there's also some mention of amd vs intel dual core. for computation using PETSc, is there any reason to buy one instead of the other? Also, supposed I use winxp + mpich2 + PETSc on a dual core, what sort of performance increase can we expect as compared to PETSc + nompi on the same machine? or is that too difficult an answer to give since there are too many factors? thank you regards
