Re: [petsc-users] PETSC Test

2017-06-14 Thread Satish Balay
The redirection is a problem with sudo - so the following is the correction echo 127.0.0.1 `hostname` | sudo tee -a /etc/hosts Satish On Thu, 15 Jun 2017, Satish Balay wrote: > The command below should work on osx aswell.. > > Satish > > On Thu, 15 Jun 2017, Mohamadreza Soltanian wrote: > >

Re: [petsc-users] Jacobian matrix for dual porosity model

2017-06-14 Thread Adrian Croucher
On 14/06/17 07:45, Jed Brown wrote: Barry Smith writes: On Jun 13, 2017, at 10:06 AM, Jed Brown wrote: Adrian Croucher writes: One way might be to form the whole Jacobian but somehow use a modified KSP solve which would implement the reduction process, do a KSP solve on the reduced system

Re: [petsc-users] PETSC Test

2017-06-14 Thread Satish Balay
The command below should work on osx aswell.. Satish On Thu, 15 Jun 2017, Mohamadreza Soltanian wrote: > Hello Satish > > Thank you for your reply. I am using macOS Sierra 10.12.5. > > Thanks > > > > On Thu, Jun 15, 2017 at 12:07 AM, Satish Balay wrote: > > > Likely its hanging in gethost

Re: [petsc-users] PETSC Test

2017-06-14 Thread Mohamadreza Soltanian
Hello Satish Thank you for your reply. I am using macOS Sierra 10.12.5. Thanks On Thu, Jun 15, 2017 at 12:07 AM, Satish Balay wrote: > Likely its hanging in gethostbyname() call - which is caued > by a mismatch in hostname. > > What OS are you using? If linux - can you do the following? > >

Re: [petsc-users] PETSC Test

2017-06-14 Thread Satish Balay
Likely its hanging in gethostbyname() call - which is caued by a mismatch in hostname. What OS are you using? If linux - can you do the following? sudo echo 127.0.0.1 `hostname` >> /etc/hosts And retry? Satish On Thu, 15 Jun 2017, Mohamadreza Soltanian wrote: > Hello All, > > I am trying to

[petsc-users] PETSC Test

2017-06-14 Thread Mohamadreza Soltanian
Hello All, I am trying to install and test PETSC. When I get to the test part, it seems everything get stuck in the following line. I was wondering if anyone can help. Thank you C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process

Re: [petsc-users] questions on BAIJ matrix

2017-06-14 Thread Barry Smith
> On Jun 8, 2017, at 2:56 PM, Xiangdong wrote: > > > On Thu, Jun 8, 2017 at 3:17 PM, Hong wrote: > Xiangdong: > MatCreateMPIBAIJWithArrays() is obviously buggy, and not been tested. > > > 1) In the remark of the function MatCreateMPIBAIJWithArrays, it says " bs - > the block size, only a bl

Re: [petsc-users] empty split for fieldsplit

2017-06-14 Thread Barry Smith
You can't do this ierr = MatSetSizes(A,PETSC_DECIDE,N,N,N);CHKERRQ(ierr); use PETSC_DECIDE for the third argument Also this is wrong for (i = Istart; i < Iend; ++i) { ierr = MatSetValue(A,i,i,2,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValue(A,i+1,i,-1,INSERT_VALUES);C

Re: [petsc-users] slepc NHEP error

2017-06-14 Thread Barry Smith
Here is the line that generates an error: ierr = MPI_Allreduce(bv->work,y,len,MPIU_SCALAR,MPIU_SUM,PetscObjectComm((PetscObject)bv));CHKERRQ(ierr); let's see what the MPI error is by running again with the additional command line option -on_error_abort hopefully MPI will say something u

Re: [petsc-users] slepc NHEP error

2017-06-14 Thread Kannan, Ramakrishnan
-- Regards, Ramki On 6/14/17, 5:21 PM, "Barry Smith" wrote: Send the file autofs/nccs-svm1_home1/ramki/libraries/slepc-3.7.3/src/sys/classes/bv/interface/bvblas.c as an attachment. Barry > On Jun 14, 2017, at 4:17 PM, Kannan, Ramakrishnan wrote: >

Re: [petsc-users] slepc NHEP error

2017-06-14 Thread Barry Smith
Send the file autofs/nccs-svm1_home1/ramki/libraries/slepc-3.7.3/src/sys/classes/bv/interface/bvblas.c as an attachment. Barry > On Jun 14, 2017, at 4:17 PM, Kannan, Ramakrishnan wrote: > > Barry, > > Appreciate your kind help. It compiles fine. I am still getting the following > err

Re: [petsc-users] slepc NHEP error

2017-06-14 Thread Kannan, Ramakrishnan
Barry, Appreciate your kind help. It compiles fine. I am still getting the following error. [0]PETSC ERROR: #1 BVDotVec_BLAS_Private() line 272 in /autofs/nccs-svm1_home1/ramki/libraries/slepc-3.7.3/src/sys/classes/bv/interface/bvblas.c [0]PETSC ERROR: #2 BVDotVec_Svec() line 150 in /autofs/nc

Re: [petsc-users] slepc NHEP error

2017-06-14 Thread Barry Smith
> On Jun 14, 2017, at 3:45 PM, Kannan, Ramakrishnan wrote: > > Barry, > > All the functions here are standard SLEPC functions and there are no > user-defined or custom code here. As you can see, when I uncomment the > CHKERRQ macros in my code, I am getting the compilation error. Yes tha

Re: [petsc-users] slepc NHEP error

2017-06-14 Thread Kannan, Ramakrishnan
Barry, All the functions here are standard SLEPC functions and there are no user-defined or custom code here. As you can see, when I uncomment the CHKERRQ macros in my code, I am getting the compilation error. -- Regards, Ramki On 6/14/17, 4:40 PM, "Barry Smith" wrote: > On Jun

Re: [petsc-users] slepc NHEP error

2017-06-14 Thread Barry Smith
> On Jun 14, 2017, at 3:33 PM, Kannan, Ramakrishnan wrote: > > Can I use CHKERRV instead of CHKERRQ? Will that help? You can do that. But I question you having functions in your code that return void instead of an error code. Without error codes you are just hurting your own productivity.

Re: [petsc-users] slepc NHEP error

2017-06-14 Thread Kannan, Ramakrishnan
Can I use CHKERRV instead of CHKERRQ? Will that help? -- Regards, Ramki On 6/14/17, 4:25 PM, "Kannan, Ramakrishnan" wrote: I get the following compilation error when I have CHKERRQ. /opt/cray/petsc/3.7.4.0/real/GNU64/5.1/sandybridge/include/petscerror.h:433:154: error: return-

Re: [petsc-users] slepc NHEP error

2017-06-14 Thread Kannan, Ramakrishnan
I get the following compilation error when I have CHKERRQ. /opt/cray/petsc/3.7.4.0/real/GNU64/5.1/sandybridge/include/petscerror.h:433:154: error: return-statement with a value, in function returning 'void' [-fpermissive] #define CHKERRQ(n) do {if (PetscUnlikely(n)) return PetscErr

Re: [petsc-users] slow generation of petsc MPIAIJ matrix

2017-06-14 Thread Barry Smith
http://www.mcs.anl.gov/petsc/documentation/faq.html#efficient-assembly > On Jun 14, 2017, at 3:18 PM, Jed Brown wrote: > > "Kannan, Ramakrishnan" writes: > >> I am running NHEP across 16 MPI processors over 16 nodes in a matrix of >> global size of 1,000,000x1,000,000 with approximately gl

Re: [petsc-users] slow generation of petsc MPIAIJ matrix

2017-06-14 Thread Jed Brown
"Kannan, Ramakrishnan" writes: > I am running NHEP across 16 MPI processors over 16 nodes in a matrix of > global size of 1,000,000x1,000,000 with approximately global 16,000,000 > non-zeros. Each node has the 1D row distribution of the matrix with exactly > 62500 rows and 1 million columns w

Re: [petsc-users] slepc NHEP error

2017-06-14 Thread Barry Smith
Why do you have the CHKERRQ(ierr); commented out in your code? Because of this you are getting mangled confusing error messages. Put a ierr = in front of all calls and a CHKERRQ(ierr); after each call. Then resend the new error message which will be much clearer. > On Jun 14, 2

[petsc-users] slow generation of petsc MPIAIJ matrix

2017-06-14 Thread Kannan, Ramakrishnan
I am running NHEP across 16 MPI processors over 16 nodes in a matrix of global size of 1,000,000x1,000,000 with approximately global 16,000,000 non-zeros. Each node has the 1D row distribution of the matrix with exactly 62500 rows and 1 million columns with 1million non-zeros as CSR/COO matrix.

Re: [petsc-users] Advice on improving Stokes Schur preconditioners

2017-06-14 Thread Dave May
On Wed, 14 Jun 2017 at 19:42, David Nolte wrote: > Dave, thanks a lot for your great answer and for sharing your experience. > I have a much clearer picture now. :) > > The experiments 3/ give the desired results for examples of cavity flow. > The (1/mu scaled) mass matrix seems OK. > > I followe

Re: [petsc-users] Beginner : question about fortran modules and makefile

2017-06-14 Thread Satish Balay
BTW: you might consider using 'master' branch from petsc git repo. The fortran module support is revamped in it. Satish On Wed, 14 Jun 2017, Satish Balay wrote: > attaching fixed files. > > $ make test > mpif90 -c -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g > -I/home/bala

Re: [petsc-users] Beginner : question about fortran modules and makefile

2017-06-14 Thread Satish Balay
attaching fixed files. $ make test mpif90 -c -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -I/home/balay/tmp/petsc/include -I/home/balay/tmp/petsc/arch-linux2-c-debug/include-o my_module.o my_module.F90 mpif90 -c -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argumen

[petsc-users] Beginner : question about fortran modules and makefile

2017-06-14 Thread Fabien Tholin
Hello, I am a beginner with Petsc and i'm trying to compile a very simple fortran program "test" with a calling program in "test.F90" and a module "my_module.F90". Unfortunately, i do not know how to write properly the makefile to be able to compile the module with "#include petsc" statements