Re: [petsc-users] Matrix format mpiaij does not have a built-in PETSc XXX!
Dear All, I hope somebody can help us on this or give at least some clearance. We have just included PETSc as an solver for our sparse matrix evolving from an unstructured mesh advection scheme. The problem is that we are using the mpiaij matrix type, since our matrix is naturally sparse. However it seems that PETSc has no PC for this, except the PCSOR, which showed to be not very effective for our problem. All others give the error msg. of the mail subject, where XXX are the different PC tried. The manual is a bit diffuse on this e.g. http://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html it is claimed that certain PC's are running on aij matrices ... but these are to be defined either as seq. or parallel (mpiaij) matrices. Moreover in the above mentioned list are two columns parallel/seriel, what is the intention of parallel capability when not applicable to matrices stored within the parallel mpiaij framework. I guess we just not understanding the concept or have some other difficulties of understanding of all this. Any comments help is welcome Aron
MPIAIJ and SEQQIJ matrices are subtypes of the AIJ matrix type. Looking at that table, you should be able to use any of the PCs that supports AIJ and has an X under 'parallel'. Max On Sun, Feb 26, 2012 at 8:16 AM, Aron Roland <[email protected]> wrote:
Dear All,
I hope somebody can help us on this or give at least some clearance.
We have just included PETSc as an solver for our sparse matrix evolving from an unstructured mesh advection scheme.
The problem is that we are using the mpiaij matrix type, since our matrix is naturally sparse. However it seems that PETSc has no PC for this, except the PCSOR, which showed to be not very effective for our problem.
All others give the error msg. of the mail subject, where XXX are the different PC tried.
The manual is a bit diffuse on this e.g.
it is claimed that certain PC's are running on aij matrices ... but these are to be defined either as seq. or parallel (mpiaij) matrices. Moreover in the above mentioned list are two columns parallel/seriel, what is the intention of parallel capability when not applicable to matrices stored within the parallel mpiaij framework.
I guess we just not understanding the concept or have some other difficulties of understanding of all this.
Any comments help is welcome
Aron
On Sun, Feb 26, 2012 at 10:48 AM, Max Rudolph <[email protected]> wrote:
MPIAIJ and SEQQIJ matrices are subtypes of the AIJ matrix type. Looking at that table, you should be able to use any of the PCs that supports AIJ and has an X under 'parallel'.
Max is correct. For instance, the most popular general purpose parallel solver is ASM (Additive Schwarz Method), which then has a sequential subsolver for each block, which defaults to ILU. Matt
Max
On Sun, Feb 26, 2012 at 8:16 AM, Aron Roland <[email protected]> wrote:
Dear All,
I hope somebody can help us on this or give at least some clearance.
We have just included PETSc as an solver for our sparse matrix evolving from an unstructured mesh advection scheme.
The problem is that we are using the mpiaij matrix type, since our matrix is naturally sparse. However it seems that PETSc has no PC for this, except the PCSOR, which showed to be not very effective for our problem.
All others give the error msg. of the mail subject, where XXX are the different PC tried.
The manual is a bit diffuse on this e.g.
it is claimed that certain PC's are running on aij matrices ... but these are to be defined either as seq. or parallel (mpiaij) matrices. Moreover in the above mentioned list are two columns parallel/seriel, what is the intention of parallel capability when not applicable to matrices stored within the parallel mpiaij framework.
I guess we just not understanding the concept or have some other difficulties of understanding of all this.
Any comments help is welcome
Aron
-- 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
Dear all, Max may be correct, but I encounter the same problem as Aron. Neither PCILU nor PCICC work in parallel for me. Here is the message I get: [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: No support for this operation for this object type! [0]PETSC ERROR: Matrix format mpiaij does not have a built-in PETSc ICC! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 6, Wed Jan 11 09:28:45 CST 2012 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. Portion of the code which I use to set the solver contents follows (I am aiming at CG+ICC combination): /* Create KPS content */ KSPCreate(PETSC_COMM_WORLD, &ksp); KSPSetType(ksp ,KSPCG); /* Set operators */ KSPSetOperators(ksp, A, A, DIFFERENT_NONZERO_PATTERN); /* Linear solver defaults (can be ove-ridden) */ KSPGetPC(ksp, &pc); PCSetType(pc, PCICC); KSPSetTolerances(ksp, 1.e-5, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT); /* Run-time options (over-rides above) */ KSPSetFromOptions(ksp); What is going wrong here? Kind regards, Bojan On 2/26/2012 6:17 PM, Matthew Knepley wrote:
On Sun, Feb 26, 2012 at 10:48 AM, Max Rudolph <[email protected] <mailto:[email protected]>> wrote:
MPIAIJ and SEQQIJ matrices are subtypes of the AIJ matrix type. Looking at that table, you should be able to use any of the PCs that supports AIJ and has an X under 'parallel'.
Max is correct. For instance, the most popular general purpose parallel solver is ASM (Additive Schwarz Method), which then has a sequential subsolver for each block, which defaults to ILU.
Matt
Max
On Sun, Feb 26, 2012 at 8:16 AM, Aron Roland <[email protected] <mailto:[email protected]>> wrote:
Dear All,
I hope somebody can help us on this or give at least some clearance.
We have just included PETSc as an solver for our sparse matrix evolving from an unstructured mesh advection scheme.
The problem is that we are using the mpiaij matrix type, since our matrix is naturally sparse. However it seems that PETSc has no PC for this, except the PCSOR, which showed to be not very effective for our problem.
All others give the error msg. of the mail subject, where XXX are the different PC tried.
The manual is a bit diffuse on this e.g.
http://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html
it is claimed that certain PC's are running on aij matrices ... but these are to be defined either as seq. or parallel (mpiaij) matrices. Moreover in the above mentioned list are two columns parallel/seriel, what is the intention of parallel capability when not applicable to matrices stored within the parallel mpiaij framework.
I guess we just not understanding the concept or have some other difficulties of understanding of all this.
Any comments help is welcome
Aron
-- 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
--
Hi Bojan, the PCILU package does not work with mpiaij matrices, same as PCICC. Basically only PCSOR works. You can install the hypre package then you can use the hypre solvers that also include an ILU PC names BILUT, however I did not had any success to achieve convergence, even if my SPARSKIT ILU-BCGSTAB converges very well. Hope this helped. Cheers Aron On 02/28/2012 08:47 AM, Bojan Niceno wrote:
Dear all,
Max may be correct, but I encounter the same problem as Aron. Neither PCILU nor PCICC work in parallel for me. Here is the message I get:
[0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: No support for this operation for this object type! [0]PETSC ERROR: Matrix format mpiaij does not have a built-in PETSc ICC! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 6, Wed Jan 11 09:28:45 CST 2012 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages.
Portion of the code which I use to set the solver contents follows (I am aiming at CG+ICC combination):
/* Create KPS content */ KSPCreate(PETSC_COMM_WORLD, &ksp); KSPSetType(ksp ,KSPCG);
/* Set operators */ KSPSetOperators(ksp, A, A, DIFFERENT_NONZERO_PATTERN);
/* Linear solver defaults (can be ove-ridden) */ KSPGetPC(ksp, &pc); PCSetType(pc, PCICC); KSPSetTolerances(ksp, 1.e-5, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
/* Run-time options (over-rides above) */ KSPSetFromOptions(ksp);
What is going wrong here?
Kind regards,
Bojan
On 2/26/2012 6:17 PM, Matthew Knepley wrote:
On Sun, Feb 26, 2012 at 10:48 AM, Max Rudolph <[email protected] <mailto:[email protected]>> wrote:
MPIAIJ and SEQQIJ matrices are subtypes of the AIJ matrix type. Looking at that table, you should be able to use any of the PCs that supports AIJ and has an X under 'parallel'.
Max is correct. For instance, the most popular general purpose parallel solver is ASM (Additive Schwarz Method), which then has a sequential subsolver for each block, which defaults to ILU.
Matt
Max
On Sun, Feb 26, 2012 at 8:16 AM, Aron Roland <[email protected] <mailto:[email protected]>> wrote:
Dear All,
I hope somebody can help us on this or give at least some clearance.
We have just included PETSc as an solver for our sparse matrix evolving from an unstructured mesh advection scheme.
The problem is that we are using the mpiaij matrix type, since our matrix is naturally sparse. However it seems that PETSc has no PC for this, except the PCSOR, which showed to be not very effective for our problem.
All others give the error msg. of the mail subject, where XXX are the different PC tried.
The manual is a bit diffuse on this e.g.
http://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html
it is claimed that certain PC's are running on aij matrices ... but these are to be defined either as seq. or parallel (mpiaij) matrices. Moreover in the above mentioned list are two columns parallel/seriel, what is the intention of parallel capability when not applicable to matrices stored within the parallel mpiaij framework.
I guess we just not understanding the concept or have some other difficulties of understanding of all this.
Any comments help is welcome
Aron
-- 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
--
On 2/28/2012 10:04 AM, Aron Roland wrote:
Hi Bojan,
the PCILU package does not work with mpiaij matrices, same as PCICC. Basically only PCSOR works.
Auch :-( When I saw your reply, I was hoping you will say: "I've found a resolution in the meantime", but you only confirmed my fears. Cheers Bojan
You can install the hypre package then you can use the hypre solvers that also include an ILU PC names BILUT, however I did not had any success to achieve convergence, even if my SPARSKIT ILU-BCGSTAB converges very well.
Hope this helped.
Cheers
Aron
On 02/28/2012 08:47 AM, Bojan Niceno wrote:
Dear all,
Max may be correct, but I encounter the same problem as Aron. Neither PCILU nor PCICC work in parallel for me. Here is the message I get:
[0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: No support for this operation for this object type! [0]PETSC ERROR: Matrix format mpiaij does not have a built-in PETSc ICC! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 6, Wed Jan 11 09:28:45 CST 2012 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages.
Portion of the code which I use to set the solver contents follows (I am aiming at CG+ICC combination):
/* Create KPS content */ KSPCreate(PETSC_COMM_WORLD, &ksp); KSPSetType(ksp ,KSPCG);
/* Set operators */ KSPSetOperators(ksp, A, A, DIFFERENT_NONZERO_PATTERN);
/* Linear solver defaults (can be ove-ridden) */ KSPGetPC(ksp, &pc); PCSetType(pc, PCICC); KSPSetTolerances(ksp, 1.e-5, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
/* Run-time options (over-rides above) */ KSPSetFromOptions(ksp);
What is going wrong here?
Kind regards,
Bojan
On 2/26/2012 6:17 PM, Matthew Knepley wrote:
On Sun, Feb 26, 2012 at 10:48 AM, Max Rudolph <[email protected] <mailto:[email protected]>> wrote:
MPIAIJ and SEQQIJ matrices are subtypes of the AIJ matrix type. Looking at that table, you should be able to use any of the PCs that supports AIJ and has an X under 'parallel'.
Max is correct. For instance, the most popular general purpose parallel solver is ASM (Additive Schwarz Method), which then has a sequential subsolver for each block, which defaults to ILU.
Matt
Max
On Sun, Feb 26, 2012 at 8:16 AM, Aron Roland <[email protected] <mailto:[email protected]>> wrote:
Dear All,
I hope somebody can help us on this or give at least some clearance.
We have just included PETSc as an solver for our sparse matrix evolving from an unstructured mesh advection scheme.
The problem is that we are using the mpiaij matrix type, since our matrix is naturally sparse. However it seems that PETSc has no PC for this, except the PCSOR, which showed to be not very effective for our problem.
All others give the error msg. of the mail subject, where XXX are the different PC tried.
The manual is a bit diffuse on this e.g.
http://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html
it is claimed that certain PC's are running on aij matrices ... but these are to be defined either as seq. or parallel (mpiaij) matrices. Moreover in the above mentioned list are two columns parallel/seriel, what is the intention of parallel capability when not applicable to matrices stored within the parallel mpiaij framework.
I guess we just not understanding the concept or have some other difficulties of understanding of all this.
Any comments help is welcome
Aron
-- 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
--
--
On Tue, Feb 28, 2012 at 3:19 AM, Bojan Niceno <[email protected]> wrote:
On 2/28/2012 10:04 AM, Aron Roland wrote:
Hi Bojan,
the PCILU package does not work with mpiaij matrices, same as PCICC. Basically only PCSOR works.
Auch :-( When I saw your reply, I was hoping you will say: "I've found a resolution in the meantime", but you only confirmed my fears.
Look, I already replied to this, and now Jed had to reply again. If you are not going to read our mail, why mail the list? Matt
Cheers
Bojan
You can install the hypre package then you can use the hypre solvers that also include an ILU PC names BILUT, however I did not had any success to achieve convergence, even if my SPARSKIT ILU-BCGSTAB converges very well.
Hope this helped.
Cheers
Aron
On 02/28/2012 08:47 AM, Bojan Niceno wrote:
Dear all,
Max may be correct, but I encounter the same problem as Aron. Neither PCILU nor PCICC work in parallel for me. Here is the message I get:
[0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: No support for this operation for this object type! [0]PETSC ERROR: Matrix format mpiaij does not have a built-in PETSc ICC! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 6, Wed Jan 11 09:28:45 CST 2012 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages.
Portion of the code which I use to set the solver contents follows (I am aiming at CG+ICC combination):
/* Create KPS content */ KSPCreate(PETSC_COMM_WORLD, &ksp); KSPSetType(ksp ,KSPCG);
/* Set operators */ KSPSetOperators(ksp, A, A, DIFFERENT_NONZERO_PATTERN);
/* Linear solver defaults (can be ove-ridden) */ KSPGetPC(ksp, &pc); PCSetType(pc, PCICC); KSPSetTolerances(ksp, 1.e-5, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
/* Run-time options (over-rides above) */ KSPSetFromOptions(ksp);
What is going wrong here?
Kind regards,
Bojan
On 2/26/2012 6:17 PM, Matthew Knepley wrote:
On Sun, Feb 26, 2012 at 10:48 AM, Max Rudolph <[email protected]> wrote:
MPIAIJ and SEQQIJ matrices are subtypes of the AIJ matrix type. Looking at that table, you should be able to use any of the PCs that supports AIJ and has an X under 'parallel'.
Max is correct. For instance, the most popular general purpose parallel solver is ASM (Additive Schwarz Method), which then has a sequential subsolver for each block, which defaults to ILU.
Matt
Max
On Sun, Feb 26, 2012 at 8:16 AM, Aron Roland <[email protected]> wrote:
Dear All,
I hope somebody can help us on this or give at least some clearance.
We have just included PETSc as an solver for our sparse matrix evolving from an unstructured mesh advection scheme.
The problem is that we are using the mpiaij matrix type, since our matrix is naturally sparse. However it seems that PETSc has no PC for this, except the PCSOR, which showed to be not very effective for our problem.
All others give the error msg. of the mail subject, where XXX are the different PC tried.
The manual is a bit diffuse on this e.g.
http://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html
it is claimed that certain PC's are running on aij matrices ... but these are to be defined either as seq. or parallel (mpiaij) matrices. Moreover in the above mentioned list are two columns parallel/seriel, what is the intention of parallel capability when not applicable to matrices stored within the parallel mpiaij framework.
I guess we just not understanding the concept or have some other difficulties of understanding of all this.
Any comments help is welcome
Aron
-- 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
--
--
-- 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
Hi all, On 2/28/2012 5:41 PM, Matthew Knepley wrote:
Look, I already replied to this, and now Jed had to reply again. If you are not going to read our mail, why mail the list?
I am reading your messages, all right, but I also read PETSc's errors and manuals. Look what the manual says on ICC: http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCICC.html "Notes: Only implemented for some matrix formats. Not implemented in parallel." And on ILU: http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCILU.html "Notes: Only implemented for some matrix formats. (for parallel see PCHYPRE <http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCHYPRE.html#PCHYPRE> for hypre's ILU)" So Matt, if I understand your answer correctly, one should use PCASM to get ILU in parallel, right? What if I want IC? Thanks, Bojan
On Tue, Feb 28, 2012 at 11:06 AM, Bojan Niceno <[email protected]> wrote:
Hi all,
On 2/28/2012 5:41 PM, Matthew Knepley wrote:
Look, I already replied to this, and now Jed had to reply again. If you are not going to read our mail, why mail the list?
I am reading your messages, all right, but I also read PETSc's errors and manuals.
Look what the manual says on ICC:
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCICC.html
"Notes: Only implemented for some matrix formats. Not implemented in parallel."
And on ILU:
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCILU.html
"Notes: Only implemented for some matrix formats. (for parallel see PCHYPRE<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCHYPRE.html#PCHYPRE>for hypre's ILU)"
So Matt, if I understand your answer correctly, one should use PCASM to get ILU in parallel, right? What if I want IC?
Or PCBJACOBI, or use Hypre for parallel ILU, or better yet do not use an unreliable preconditioner with poor scalability. How does this lead you to conclude that SOR is the only thing you can run in parallel? Matt
Thanks,
Bojan
-- 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
Dear all, I try to configure Petsc to use HDF5. During the HDF5 compilation stage the memory use increases untill the computer basically stalls and almost all memory is used. After 2500s the compilation is stopped because of a runaway process. Did somebody encounter this before? How can I solve this? Thanks for your input! Kind regards, Steven
On Wed, Feb 29, 2012 at 15:35, Haren, S.W. van (Steven) <[email protected]>wrote:
Dear all,
I try to configure Petsc to use HDF5.
During the HDF5 compilation stage the memory use increases untill the computer basically stalls and almost all memory is used. After 2500s the compilation is stopped because of a runaway process.
Check configure.log and/or attach a debugger to find out where it got stuck. At least use "top" to find out which process is taking all the time and memory.
Dear Jed, Thanks for your reply. These are the last lines from the configure.log: sh: cd /home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6 && make clean && make && make install Executing: cd /home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6 && make clean && make && make install Runaway process exceeded time limit of 2500s sh: ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Error running make on HDF5: Could not execute "cd /home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6 && make clean && make && make install": Runaway process exceeded time limit of 2500s ******************************************************************************* File "./config/configure.py", line 283, in petsc_configure framework.configure(out = sys.stdout) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/framework.py", line 925, in configure child.configure() File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 506, in configure self.executeTest(self.configureLibrary) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/base.py", line 115, in executeTest ret = apply(test, args,kargs) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/packages/hdf5.py", line 63, in configureLibrary config.package.Package.configureLibrary(self) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 433, in configureLibrary for location, directory, lib, incl in self.generateGuesses(): File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 228, in generateGuesses d = self.checkDownload(1) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 313, in checkDownload return self.getInstallDir() File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 183, in getInstallDir return os.path.abspath(self.Install()) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/packages/hdf5.py", line 56, in Install raise RuntimeError('Error running make on HDF5: '+str(e)) Using the top command I cannot really identify a process that uses all the memory. The memory use increases untill completely full. But the maximum percentage used by any process does not go above 10 percent. Even when the compilation is stopped the memory is not freed. I don't really understand this. Could you give me a few pointers based on the configure.log output? Hoe should I attach a debugger? Any good links were I can read how to do that? Thanks in advance. Kind regards, Steven -----Original Message----- From: [email protected] on behalf of Jed Brown Sent: Wed 2/29/2012 10:43 PM To: PETSc users list Subject: Re: [petsc-users] HDF5 installation problems On Wed, Feb 29, 2012 at 15:35, Haren, S.W. van (Steven) <[email protected]>wrote:
Dear all,
I try to configure Petsc to use HDF5.
During the HDF5 compilation stage the memory use increases untill the computer basically stalls and almost all memory is used. After 2500s the compilation is stopped because of a runaway process.
Check configure.log and/or attach a debugger to find out where it got stuck. At least use "top" to find out which process is taking all the time and memory.
On Sun, Mar 4, 2012 at 05:43, Haren, S.W. van (Steven) <[email protected]>wrote:
Dear Jed,
Thanks for your reply.
These are the last lines from the configure.log:
sh: cd /home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6 && make clean && make && make install Executing: cd /home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6 && make clean && make && make install Runaway process exceeded time limit of 2500s
Possibilities: 1. System clock was changed or the machine was suspended, causing incorrect timeout. (As an aside, the Python docs are horrible. They act like time is one thing, so I have to read the source code to find out that threading.Thread.join() implements a timeout using time(2) which is neither monotone nor continuous.) 2. The compilation actually takes a long time on this machine, perhaps because it doesn't get much time to run due to other jobs. You could try increasing the timeout or running make manually from externalpackages/hdf5-1.8.6/. 3. The hdf5 build process is getting stuck somewhere, I suggest trying to complete the install manually from externalpackages/hdf5-1.8.6/. If you can't get it working, send configure.log and HDF5 attempted build logs to [email protected].
sh:
******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
------------------------------------------------------------------------------- Error running make on HDF5: Could not execute "cd /home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6 && make clean && make && make install": Runaway process exceeded time limit of 2500s
******************************************************************************* File "./config/configure.py", line 283, in petsc_configure framework.configure(out = sys.stdout) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/framework.py", line 925, in configure child.configure() File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 506, in configure self.executeTest(self.configureLibrary) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/base.py", line 115, in executeTest ret = apply(test, args,kargs) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/packages/hdf5.py", line 63, in configureLibrary config.package.Package.configureLibrary(self) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 433, in configureLibrary for location, directory, lib, incl in self.generateGuesses(): File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 228, in generateGuesses d = self.checkDownload(1) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 313, in checkDownload return self.getInstallDir() File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 183, in getInstallDir return os.path.abspath(self.Install()) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/packages/hdf5.py", line 56, in Install raise RuntimeError('Error running make on HDF5: '+str(e))
Using the top command I cannot really identify a process that uses all the memory. The memory use increases untill completely full. But the maximum percentage used by any process does not go above 10 percent. Even when the compilation is stopped the memory is not freed. I don't really understand this. Could you give me a few pointers based on the configure.log output?
Hoe should I attach a debugger? Any good links were I can read how to do that?
Thanks in advance.
Kind regards,
Steven
-----Original Message----- From: [email protected] on behalf of Jed Brown Sent: Wed 2/29/2012 10:43 PM To: PETSc users list Subject: Re: [petsc-users] HDF5 installation problems
On Wed, Feb 29, 2012 at 15:35, Haren, S.W. van (Steven) <[email protected]
wrote:
Dear all,
I try to configure Petsc to use HDF5.
During the HDF5 compilation stage the memory use increases untill the computer basically stalls and almost all memory is used. After 2500s the compilation is stopped because of a runaway process.
Check configure.log and/or attach a debugger to find out where it got stuck. At least use "top" to find out which process is taking all the time and memory.
Dear Jed, Thanks for your help. After some more investigation it turned out that hdf5 was testing its parallel abilities with 6 processes during the testing if (if I installed it via PETSC configure). After this I installed hdf5 manually and then configured Petsc using: ./configure --with-shared-libraries --with-hdf5-lib=/home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6/hdf5/lib/libhdf5.so --with-hdf5 --with-hdf5-include=/home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6/hdf5/include/ Now it works like a charm! Thanks again for your help. Kind regards, Steven -----Original Message----- From: [email protected] on behalf of Jed Brown Sent: Sun 3/4/2012 3:15 PM To: PETSc users list Subject: Re: [petsc-users] HDF5 installation problems On Sun, Mar 4, 2012 at 05:43, Haren, S.W. van (Steven) <[email protected]>wrote:
Dear Jed,
Thanks for your reply.
These are the last lines from the configure.log:
sh: cd /home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6 && make clean && make && make install Executing: cd /home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6 && make clean && make && make install Runaway process exceeded time limit of 2500s
Possibilities: 1. System clock was changed or the machine was suspended, causing incorrect timeout. (As an aside, the Python docs are horrible. They act like time is one thing, so I have to read the source code to find out that threading.Thread.join() implements a timeout using time(2) which is neither monotone nor continuous.) 2. The compilation actually takes a long time on this machine, perhaps because it doesn't get much time to run due to other jobs. You could try increasing the timeout or running make manually from externalpackages/hdf5-1.8.6/. 3. The hdf5 build process is getting stuck somewhere, I suggest trying to complete the install manually from externalpackages/hdf5-1.8.6/. If you can't get it working, send configure.log and HDF5 attempted build logs to [email protected].
sh:
******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
------------------------------------------------------------------------------- Error running make on HDF5: Could not execute "cd /home/steven/C++/PETSc/petsc-3.2-p6/externalpackages/hdf5-1.8.6 && make clean && make && make install": Runaway process exceeded time limit of 2500s
******************************************************************************* File "./config/configure.py", line 283, in petsc_configure framework.configure(out = sys.stdout) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/framework.py", line 925, in configure child.configure() File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 506, in configure self.executeTest(self.configureLibrary) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/base.py", line 115, in executeTest ret = apply(test, args,kargs) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/packages/hdf5.py", line 63, in configureLibrary config.package.Package.configureLibrary(self) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 433, in configureLibrary for location, directory, lib, incl in self.generateGuesses(): File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 228, in generateGuesses d = self.checkDownload(1) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 313, in checkDownload return self.getInstallDir() File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/package.py", line 183, in getInstallDir return os.path.abspath(self.Install()) File "/home/steven/C++/PETSc/petsc-3.2-p6/config/BuildSystem/config/packages/hdf5.py", line 56, in Install raise RuntimeError('Error running make on HDF5: '+str(e))
Using the top command I cannot really identify a process that uses all the memory. The memory use increases untill completely full. But the maximum percentage used by any process does not go above 10 percent. Even when the compilation is stopped the memory is not freed. I don't really understand this. Could you give me a few pointers based on the configure.log output?
Hoe should I attach a debugger? Any good links were I can read how to do that?
Thanks in advance.
Kind regards,
Steven
-----Original Message----- From: [email protected] on behalf of Jed Brown Sent: Wed 2/29/2012 10:43 PM To: PETSc users list Subject: Re: [petsc-users] HDF5 installation problems
On Wed, Feb 29, 2012 at 15:35, Haren, S.W. van (Steven) <[email protected]
wrote:
Dear all,
I try to configure Petsc to use HDF5.
During the HDF5 compilation stage the memory use increases untill the computer basically stalls and almost all memory is used. After 2500s the compilation is stopped because of a runaway process.
Check configure.log and/or attach a debugger to find out where it got stuck. At least use "top" to find out which process is taking all the time and memory.
On Tue, Feb 28, 2012 at 03:04, Aron Roland <[email protected]>wrote:
the PCILU package does not work with mpiaij matrices, same as PCICC. Basically only PCSOR works.
Hardly, there are lots of parallel preconditioners tabulated in the solver table. Since you don't seem to be clicking the links to man pages or looking at examples, here are some concrete examples. # Additive Schwarz with various subdomain solvers -pc_type asm -sub_pc_type icc -pc_type asm -sub_pc_type ilu -pc_type asm -sub_pc_type lu # Block Jacobi (equivalent to zero-overlap additive Schwarz) -pc_type bjacobi -sub_pc_type icc # Redundant direct solve (useful for coarse levels or for debugging) -pc_type redundant -redundant_pc_type lu # Parallel direct solve (with various packages) -pc_type lu -pc_factor_mat_solver_package mumps -pc_type lu -pc_factor_mat_solver_package superlu_dist -pc_type lu -pc_factor_mat_solver_package pastix # Parallel smoothed aggregation algebraic multigrid -pc_type gamg # requires petsc-dev -pc_type ml # --download-ml # Classical algebraic multigrid (from Hypre) -pc_type hypre -pc_hypre_type boomeramg # Parallel ILU -pc_type hypre -pc_hypre_type pilut # deprecated, but includes drop tolerance -pc_type hypre -pc_hypre_type euclid # supported, no drop tolerance # Sparse approximate inverse -pc_type spai -pc_type hypre -pc_hypre_type parasails # Field split with AMG inside (physics-blocked relaxation (Schwarz) or factorization (Schur)) -pc_type fieldsplit -fieldsplit_0_pc_type gamg -fieldsplit_1_pc_type pbjacobi # Factorization field split with automatic saddle point detection, precondition Schur complement with least squares commutator -pc_type fieldsplit -pc_fieldsplit_detect_saddle_point -pc_fieldsplit_type schur -fieldsplit_0_pc_type gamg -fieldsplit_1_pc_type ls -fieldsplit_1_lsc_pc_type gamg and so on...
participants (7)
-
Aron Roland -
Aron Roland -
Bojan Niceno -
Haren, S.W. van (Steven) -
Jed Brown -
Matthew Knepley -
Max Rudolph