Re: [petsc-users] duplicated libs

And to have cleaner list - specify the (appropriate) compiler libraries via LIBS option balay@pj01:~/petsc$ mpif90 -show gfortran -I/software/mpich-4.1.1/include -I/software/mpich-4.1.1/include -L/software/mpich-4.1.1/lib -lmpifort -Wl,-rpath -Wl,/software/mpich-4.1.1/lib -Wl,--enable-new-dtags

Re: [petsc-users] duplicated libs

You can try using latest petsc version [3.21] - the list should be a bit more cleaner with it. balay@pj01:~/petsc$ ./configure --download-mpich --download-fblaslapack --download-hdf5 --with-hdf5-fortran-bindings --download-metis --download-parmetis COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 -

[petsc-users] DMPlex periodic face coordinates

Dear petsc-users,     I am playing with DMPlexGetCellCoordinates and observing that it returns correct periodic coordinates for cells, but not for faces. More precisely, adding PetscCall(DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd));     for (f = fStart; f < fEnd; ++f) {   const PetscSca

Re: [petsc-users] duplicated libs

It is not always safe to remove duplicate libraries listed in different places in the list. Hence we cannot simply always remove them. Barry > On May 13, 2024, at 10:00 PM, Runjian Wu wrote: > > Thanks for your reply! Since I can manually remove duplicates, how about > adding a function

Re: [petsc-users] VecGetArrayF90 vs. VecGetArrayReadF90

It errors in C because the argument is labeled with const, but there does not seem to be a way in Fortran to indicate an array is read only. > On May 13, 2024, at 10:21 PM, Runjian Wu wrote: > > I only know the "intent(in)" attribute for the dummy arguments. > > In the counter function V

Re: [petsc-users] duplicated libs

First clarification, NO issues happened. I am just curious about the duplicated libraries while I compile PFLOTRAN with PETSc. PETSc version: 3.16.2 Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --with-make-np=4 --with-cc=mpicc --with-cxx=mpicxx --with-

Re: [petsc-users] GMSH entities

On 14/05/24 1:44 pm, Matthew Knepley wrote: I wish GMsh was clearer about what is optional: https://urldefense.us/v3/__https://gmsh.info/doc/texinfo/gmsh.html*MSH-file-format__;Iw!!G_uCfscf7eWS!aCypJMAzwWHAJLXGNJmSthDjbHcU-8_MdsaXZ4d1r1RKyL0bqIv5ZuLmQtV6ve4XcTjapf38-bsdDOLEDAlhWoaaGpmjDCYs$

Re: [petsc-users] duplicated libs

Thanks for your reply! Since I can manually remove duplicates, how about adding a function to automatically remove duplicates at the end of "configure" in the next PETSc version? Runjian On 5/13/2024 9:31 PM, Barry Smith wrote: Because the order of the libraries can be important, it is dif

Re: [petsc-users] GMSH entities

On Mon, May 13, 2024 at 9:33 PM Adrian Croucher wrote: > hi, We often create meshes in GMSH format using the meshio library. This > works OK if we stick to GMSH file format 2. 2. If we use GMSH file format > 4. 1, DMPlex can't read them because it expects the "Entities" section to > be present: [

[petsc-users] GMSH entities

hi, We often create meshes in GMSH format using the meshio library. This works OK if we stick to GMSH file format 2. 2. If we use GMSH file format 4. 1, DMPlex can't read them because it expects the "Entities" section to be present: [0]PETSC ZjQcmQRYFpfptBannerStart Thi

Re: [petsc-users] Using Compute-Sanitizer with PETSc

Depending on your mpi mpiexec is not needed so compute-sanitizer --tool memcheck --leak-check full ./a.out args may work > On May 13, 2024, at 8:16 PM, Sreeram R Venkat wrote: > > This Message Is From an External Sender > This message came from outside your organization. > I am trying t

[petsc-users] Using Compute-Sanitizer with PETSc

I am trying to check my program for GPU memory leaks with the compute-sanitizer tool. If I run my application with: mpiexec -n 1 compute-sanitizer --tool memcheck --leak-check full ./a.out args I get the message: Error: No attachable process found. compute-sanitizer timed-out. Adding --target-pro

Re: [petsc-users] [SLEPc] Best method to compute all eigenvalues of a MatShell

I also just ran with cupy.linalg.eigvalsh (which wraps cuSOLVER), and it only took 3.1 seconds. I will probably use this, but it is good to know about the SLEPc cases if I don't need the full spectrum or have sparse matrices, etc. Thanks, Sreeram On Mon, May 13, 2024 at 2:13 PM Sreeram R Venkat

Re: [petsc-users] [SLEPc] Best method to compute all eigenvalues of a MatShell

Apologies, I accidentally hit "reply" instead of "reply-all." Thank you for the reference. Actually, I just tested that N ~ 1e4 case where I had saved the dense matrix to a python-readable format. Using scipy.linalg.eigvalsh, I got the eigenvalues in ~1.5 minutes. They agree with the ones I got fr

Re: [petsc-users] [SLEPc] Best method to compute all eigenvalues of a MatShell

Please respond to the list. The mpd parameter means "maximum projected dimension". You can think of the projected problem as the "sequential" part of the computation, that is not parallelized ("small" dense eigenproblem). When you run with ZjQcmQRYFpfptBannerStart This

Re: [petsc-users] Can not find the header file for OpenMPI

Thanks a lot. That is the only issue. /usr/lib64/openmpi/include doesn't exist. The configuration can be done without issue with the 2nd method. But when I did make, the following warning came. I will study your link. Thanks, f951: Warning: Nonexistent include directory ‘/usr/lib64/openmpi/inclu

Re: [petsc-users] [SLEPc] Best method to compute all eigenvalues of a MatShell

Computing the full spectrum is always an unpleasant task. But if you cannot avoid it, I would suggest that you compute the eigenvalues in two runs: n/2 largest real eigenvalues and n/2 smallest real. If your matrix-vector product is cheap, ZjQcmQRYFpfptBannerStart This

Re: [petsc-users] [SLEPc] Best method to compute all eigenvalues of a MatShell

On Mon, May 13, 2024 at 1:40 PM Sreeram R Venkat wrote: > I have a MatShell object that computes matrix-vector products of a dense > symmetric matrix of size NxN. The MatShell does not actually form the dense > matrix, so it is never in memory/storage. For my application, N ranges from > 1e4 to 1

Re: [petsc-users] Can not find the header file for OpenMPI

> Includes: -I/usr/lib64/openmpi/include (*This is not the right include > directory*) So this is the only issue? Does this dir not exist? If so, you can try the following fix: https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7545__;!!G_uCfscf7eWS!a7OhWBQn8Zp5RfRnL

[petsc-users] [SLEPc] Best method to compute all eigenvalues of a MatShell

I have a MatShell object that computes matrix-vector products of a dense symmetric matrix of size NxN. The MatShell does not actually form the dense matrix, so it is never in memory/storage. For my application, N ranges from 1e4 to 1e5. I want to compute the full spectrum of this matrix. For an ex

Re: [petsc-users] Can not find the header file for OpenMPI

On Mon, 13 May 2024, neil liu wrote: > I also tried the 2nd way, it didn't work. configure.log attached is successful. Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --download-fblaslapack --with-mpi-dir=/usr/lib64/openmpi Compilers: C Co

Re: [petsc-users] Can not find the header file for OpenMPI

If you are using mpicc/mpif90 as compilers from you pre-installed MPI - you don't need to list --with-mpi-include, --with-mpi-lib options. As mentioned - you can do this either with: [if you have then in PATH] --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 or: --with-cc=MPI-DIR/bin/mpicc -

Re: [petsc-users] Can not find the header file for OpenMPI

Thanks. I want to use the preinstalled OpenMPI to configure petsc. For the preinstalled OpenMPI, the lib and include dir are at different places. Then how should I configure with this preinstalled OpenMPI? Thanks, $ mpicc --show gcc -I/usr/include/openmpi-x86_64 -Wl,-rpath -Wl,/usr/lib64/openmpi/

Re: [petsc-users] Can not find the header file for OpenMPI

You are misinterpreting --with-mpi-include --with-mpi-lib options. Any particular reason you want to use these options instead of mpi compilers? >>> balay@p1 /home/balay $ mpicc -show gcc -I/home/balay/soft/mpich-4.0.1/include -L/home/balay/soft/mpich-4.0.1/lib -Wl,-rpath -Wl,/home/balay/so

Re: [petsc-users] Can not find the header file for OpenMPI

On Mon, 13 May 2024, neil liu wrote: > Dear Petsc developers, > > I am trying to install Petsc with a preinstalled OpenMPi. > > ./configure --download-fblaslapack --with-mpi-dir=/usr/lib64/openmpi --with-mpi-dir=DIR is a bit unique [wrt other pkg-dir options]. It means: --with-cc=DIR/bin/mp

[petsc-users] Can not find the header file for OpenMPI

Dear Petsc developers, I am trying to install Petsc with a preinstalled OpenMPi. ./configure --download-fblaslapack --with-mpi-dir=/usr/lib64/openmpi --with-mpi-incdir=/usr/include/openmpi-x86_64 But the final information shows, MPI: Version:3 Includes: -I/usr/lib64/openmpi/include (

Re: [petsc-users] VecGetArrayF90 vs. VecGetArrayReadF90

I couldn't find a way in Fortran to declare an array as read-only. Is there such support? Barry > On May 13, 2024, at 7:28 AM, Runjian Wu wrote: > > This Message Is From an External Sender > This message came from outside your organization. > Hi all, > > I have a question about VecGet

Re: [petsc-users] duplicated libs

what version of PETSc? What configure command? What do you have for PETSC_EXTERNAL_LIB_BASIC? You can send configure.log for your build to petsc-maint Generally duplicates should not cause grief. [as one needs them to overcome circular dependencies]. What issues are you seeing? [send relevant

Re: [petsc-users] duplicated libs

Because the order of the libraries can be important, it is difficult for ./configure to remove unneeded duplicates automatically. You can manually remove duplicates by editing $PETSC_ARCH/lib/petsc/conf/petscvariables after running ./configure Barry > On May 13, 2024, at 7:47 AM, R

[petsc-users] VecGetArrayF90 vs. VecGetArrayReadF90

Hi all, I have a question about VecGetArrayReadF90(...). If I use VecGetArrayReadF90(...), I can still write entries into the array like VecGetArrayF90(...). Is it possible to report an error during compile process? Thanks, Runjian Wu

[petsc-users] duplicated libs

Hi all, After I compiled PETSc, I found some duplicated libs in the variable PETSC_EXTERNAL_LIB_BASIC, e.g., -lm, -lgfortran -lstdc++. I am curious how it happened and how to remove the duplicates? Thanks, Runjian Wu

Re: [petsc-users] HDF5 time step count

On Sun, May 12, 2024 at 10:42 PM Adrian Croucher wrote: > hi Matt, > On 11/05/24 4:12 am, Matthew Knepley wrote: > > Thanks. I tried it out and the error below was raised, looks like it's >> when it tries to destroy the viewer. It still runs ok when >> DMGetOutputSequenceLength() isn't called. >>