Hello, I am trying to build petsc4py-3.5.1 using Cygwin on 64-bit Windows 7. I have built PETSc 3.5.4 with shared and dynamic libraries using mpich2-1.2.1 and successfully ran the installation tests. I am using Python 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I attempt to install petsc4py (both with pip and distutils) I get a mpicc compiler error due to undefined references/symbols. I have attached the output of running pip install petsc petsc4py --allow-external petsc --allow-external petsc4py Thank you in advance for any help, Mikhail Khodak
On 8 June 2015 at 02:50, Mikhail Khodak <[email protected]> wrote:
Hello, I am trying to build petsc4py-3.5.1 using Cygwin on 64-bit Windows 7. I have built PETSc 3.5.4 with shared and dynamic libraries using mpich2-1.2.1 and successfully ran the installation tests. I am using Python 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I attempt to install petsc4py (both with pip and distutils) I get a mpicc compiler error due to undefined references/symbols. I have attached the output of running
pip install petsc petsc4py --allow-external petsc --allow-external petsc4py
I've never ever built or test petsc4py under Cygwin. The errors you see are expected. Perhaps you can manually workaround the issues following the following steps: 1) Download the petsc4py tarball and unpack it. 2) Open the file "src/libpetsc4py/libpetsc4py.h", add remove all occurences of DL_IMPORT, i.e, replace DL_IMPORT(XYZ) for just XYZ 3) Use pip again: pip install petsc pip install . The last line assumes your current working directory is the one having petsc4py's setup.py Finally, I do not guarantee this will work. I'm just guessing, petsc4py never explicitly supported Windows and/or Cygwin. -- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Thank you for your help - the install seems to work, apart from routines requiring MPI, which fail due to the "Attempting to use an MPI routine before initializing MPI" error. This seems to be an error in the PETSc build itself. Thanks again, Mikhail Khodak On Mon, Jun 8, 2015 at 5:11 AM, Lisandro Dalcin <[email protected]> wrote:
On 8 June 2015 at 02:50, Mikhail Khodak <[email protected]> wrote:
Hello, I am trying to build petsc4py-3.5.1 using Cygwin on 64-bit Windows 7. I have built PETSc 3.5.4 with shared and dynamic libraries using mpich2-1.2.1 and successfully ran the installation tests. I am using Python 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I attempt to install petsc4py (both with pip and distutils) I get a mpicc compiler error due to undefined references/symbols. I have attached the output of running
pip install petsc petsc4py --allow-external petsc --allow-external petsc4py
I've never ever built or test petsc4py under Cygwin. The errors you see are expected. Perhaps you can manually workaround the issues following the following steps:
1) Download the petsc4py tarball and unpack it. 2) Open the file "src/libpetsc4py/libpetsc4py.h", add remove all occurences of DL_IMPORT, i.e, replace DL_IMPORT(XYZ) for just XYZ 3) Use pip again:
pip install petsc pip install .
The last line assumes your current working directory is the one having petsc4py's setup.py
Finally, I do not guarantee this will work. I'm just guessing, petsc4py never explicitly supported Windows and/or Cygwin.
-- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
On Thu, Jun 11, 2015 at 5:07 AM, Mikhail Khodak <[email protected]> wrote:
Thank you for your help - the install seems to work, apart from routines requiring MPI, which fail due to the "Attempting to use an MPI routine before initializing MPI" error. This seems to be an error in the PETSc build itself.
The MPI routines will not work until after import petsc4py, sys petsc4py.init(sys.argv) from petsc4py import PETSc If they fail after this, it is usually a mismatch between the mpiexec being used and the MPI libraries being linked. Thanks, Matt Thanks again,
Mikhail Khodak
On Mon, Jun 8, 2015 at 5:11 AM, Lisandro Dalcin <[email protected]> wrote:
On 8 June 2015 at 02:50, Mikhail Khodak <[email protected]> wrote:
Hello, I am trying to build petsc4py-3.5.1 using Cygwin on 64-bit Windows 7. I have built PETSc 3.5.4 with shared and dynamic libraries using mpich2-1.2.1 and successfully ran the installation tests. I am using Python 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I attempt to install petsc4py (both with pip and distutils) I get a mpicc compiler error due to undefined references/symbols. I have attached the output of running
pip install petsc petsc4py --allow-external petsc --allow-external petsc4py
I've never ever built or test petsc4py under Cygwin. The errors you see are expected. Perhaps you can manually workaround the issues following the following steps:
1) Download the petsc4py tarball and unpack it. 2) Open the file "src/libpetsc4py/libpetsc4py.h", add remove all occurences of DL_IMPORT, i.e, replace DL_IMPORT(XYZ) for just XYZ 3) Use pip again:
pip install petsc pip install .
The last line assumes your current working directory is the one having petsc4py's setup.py
Finally, I do not guarantee this will work. I'm just guessing, petsc4py never explicitly supported Windows and/or Cygwin.
-- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
-- 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
I added these lines to the petsc4py test files (specifically test_comm.py) but the error remains the same. However, I have done the standard 'which mpiexec', 'which mpicc', 'which mpirun' and they are all in the same folder. In fact it is the only MPI installed. The reason I thought it might be a PETSc build problem is because one of the PETSc 'make test' tests (ex5f) fails with the same error, even though the 'make streams' test works fine with MPI processes. Thanks, Mikhail On Thu, Jun 11, 2015 at 4:21 AM, Matthew Knepley <[email protected]> wrote:
On Thu, Jun 11, 2015 at 5:07 AM, Mikhail Khodak <[email protected]> wrote:
Thank you for your help - the install seems to work, apart from routines requiring MPI, which fail due to the "Attempting to use an MPI routine before initializing MPI" error. This seems to be an error in the PETSc build itself.
The MPI routines will not work until after
import petsc4py, sys petsc4py.init(sys.argv) from petsc4py import PETSc
If they fail after this, it is usually a mismatch between the mpiexec being used and the MPI libraries being linked.
Thanks,
Matt
Thanks again,
Mikhail Khodak
On Mon, Jun 8, 2015 at 5:11 AM, Lisandro Dalcin <[email protected]> wrote:
On 8 June 2015 at 02:50, Mikhail Khodak <[email protected]> wrote:
Hello, I am trying to build petsc4py-3.5.1 using Cygwin on 64-bit Windows 7. I have built PETSc 3.5.4 with shared and dynamic libraries using mpich2-1.2.1 and successfully ran the installation tests. I am using Python 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I attempt to install petsc4py (both with pip and distutils) I get a mpicc compiler error due to undefined references/symbols. I have attached the output of running
pip install petsc petsc4py --allow-external petsc --allow-external petsc4py
I've never ever built or test petsc4py under Cygwin. The errors you see are expected. Perhaps you can manually workaround the issues following the following steps:
1) Download the petsc4py tarball and unpack it. 2) Open the file "src/libpetsc4py/libpetsc4py.h", add remove all occurences of DL_IMPORT, i.e, replace DL_IMPORT(XYZ) for just XYZ 3) Use pip again:
pip install petsc pip install .
The last line assumes your current working directory is the one having petsc4py's setup.py
Finally, I do not guarantee this will work. I'm just guessing, petsc4py never explicitly supported Windows and/or Cygwin.
-- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
-- 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
If you get errors when running basic petsc examples - send us the relavant petsc logs [configure.log, make.log, test.log etc..] Also - note that mpich is not supported on cygwin/windows [it generally works for us - when we try the --download-mpich build]. Unless you really need a cywin build/use of petsc4py - it might be easier to install a linux VM - and use PETSc/petsc4py on it. Satish On Thu, 11 Jun 2015, Mikhail Khodak wrote:
I added these lines to the petsc4py test files (specifically test_comm.py) but the error remains the same. However, I have done the standard 'which mpiexec', 'which mpicc', 'which mpirun' and they are all in the same folder. In fact it is the only MPI installed. The reason I thought it might be a PETSc build problem is because one of the PETSc 'make test' tests (ex5f) fails with the same error, even though the 'make streams' test works fine with MPI processes. Thanks, Mikhail
On Thu, Jun 11, 2015 at 4:21 AM, Matthew Knepley <[email protected]> wrote:
On Thu, Jun 11, 2015 at 5:07 AM, Mikhail Khodak <[email protected]> wrote:
Thank you for your help - the install seems to work, apart from routines requiring MPI, which fail due to the "Attempting to use an MPI routine before initializing MPI" error. This seems to be an error in the PETSc build itself.
The MPI routines will not work until after
import petsc4py, sys petsc4py.init(sys.argv) from petsc4py import PETSc
If they fail after this, it is usually a mismatch between the mpiexec being used and the MPI libraries being linked.
Thanks,
Matt
Thanks again,
Mikhail Khodak
On Mon, Jun 8, 2015 at 5:11 AM, Lisandro Dalcin <[email protected]> wrote:
On 8 June 2015 at 02:50, Mikhail Khodak <[email protected]> wrote:
Hello, I am trying to build petsc4py-3.5.1 using Cygwin on 64-bit Windows 7. I have built PETSc 3.5.4 with shared and dynamic libraries using mpich2-1.2.1 and successfully ran the installation tests. I am using Python 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I attempt to install petsc4py (both with pip and distutils) I get a mpicc compiler error due to undefined references/symbols. I have attached the output of running
pip install petsc petsc4py --allow-external petsc --allow-external petsc4py
I've never ever built or test petsc4py under Cygwin. The errors you see are expected. Perhaps you can manually workaround the issues following the following steps:
1) Download the petsc4py tarball and unpack it. 2) Open the file "src/libpetsc4py/libpetsc4py.h", add remove all occurences of DL_IMPORT, i.e, replace DL_IMPORT(XYZ) for just XYZ 3) Use pip again:
pip install petsc pip install .
The last line assumes your current working directory is the one having petsc4py's setup.py
Finally, I do not guarantee this will work. I'm just guessing, petsc4py never explicitly supported Windows and/or Cygwin.
-- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
-- 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
Also - should mention: - cygwin has OpenMPI pacakged - so you could also try that. - most of my builds are static [so never tried dll builds] Satish On Thu, 11 Jun 2015, Satish Balay wrote:
If you get errors when running basic petsc examples - send us the relavant petsc logs [configure.log, make.log, test.log etc..]
Also - note that mpich is not supported on cygwin/windows [it generally works for us - when we try the --download-mpich build].
Unless you really need a cywin build/use of petsc4py - it might be easier to install a linux VM - and use PETSc/petsc4py on it.
Satish
On Thu, 11 Jun 2015, Mikhail Khodak wrote:
I added these lines to the petsc4py test files (specifically test_comm.py) but the error remains the same. However, I have done the standard 'which mpiexec', 'which mpicc', 'which mpirun' and they are all in the same folder. In fact it is the only MPI installed. The reason I thought it might be a PETSc build problem is because one of the PETSc 'make test' tests (ex5f) fails with the same error, even though the 'make streams' test works fine with MPI processes. Thanks, Mikhail
On Thu, Jun 11, 2015 at 4:21 AM, Matthew Knepley <[email protected]> wrote:
On Thu, Jun 11, 2015 at 5:07 AM, Mikhail Khodak <[email protected]> wrote:
Thank you for your help - the install seems to work, apart from routines requiring MPI, which fail due to the "Attempting to use an MPI routine before initializing MPI" error. This seems to be an error in the PETSc build itself.
The MPI routines will not work until after
import petsc4py, sys petsc4py.init(sys.argv) from petsc4py import PETSc
If they fail after this, it is usually a mismatch between the mpiexec being used and the MPI libraries being linked.
Thanks,
Matt
Thanks again,
Mikhail Khodak
On Mon, Jun 8, 2015 at 5:11 AM, Lisandro Dalcin <[email protected]> wrote:
On 8 June 2015 at 02:50, Mikhail Khodak <[email protected]> wrote:
Hello, I am trying to build petsc4py-3.5.1 using Cygwin on 64-bit Windows 7. I have built PETSc 3.5.4 with shared and dynamic libraries using mpich2-1.2.1 and successfully ran the installation tests. I am using Python 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I attempt to install petsc4py (both with pip and distutils) I get a mpicc compiler error due to undefined references/symbols. I have attached the output of running
pip install petsc petsc4py --allow-external petsc --allow-external petsc4py
I've never ever built or test petsc4py under Cygwin. The errors you see are expected. Perhaps you can manually workaround the issues following the following steps:
1) Download the petsc4py tarball and unpack it. 2) Open the file "src/libpetsc4py/libpetsc4py.h", add remove all occurences of DL_IMPORT, i.e, replace DL_IMPORT(XYZ) for just XYZ 3) Use pip again:
pip install petsc pip install .
The last line assumes your current working directory is the one having petsc4py's setup.py
Finally, I do not guarantee this will work. I'm just guessing, petsc4py never explicitly supported Windows and/or Cygwin.
-- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
-- 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
I have attached the log files. I tried using Open MPI before but received the same result. I will try a static build later and otherwise will get a VM. Thanks for looking at this, Mikhail On Thu, Jun 11, 2015 at 10:48 AM, Satish Balay <[email protected]> wrote:
Also - should mention:
- cygwin has OpenMPI pacakged - so you could also try that. - most of my builds are static [so never tried dll builds]
Satish
On Thu, 11 Jun 2015, Satish Balay wrote:
If you get errors when running basic petsc examples - send us the relavant petsc logs [configure.log, make.log, test.log etc..]
Also - note that mpich is not supported on cygwin/windows [it generally works for us - when we try the --download-mpich build].
Unless you really need a cywin build/use of petsc4py - it might be easier to install a linux VM - and use PETSc/petsc4py on it.
Satish
On Thu, 11 Jun 2015, Mikhail Khodak wrote:
I added these lines to the petsc4py test files (specifically test_comm.py) but the error remains the same. However, I have done the standard 'which mpiexec', 'which mpicc', 'which mpirun' and they are all in the same folder. In fact it is the only MPI installed. The reason I thought it might be a PETSc build problem is because one of the PETSc 'make test' tests (ex5f) fails with the same error, even though the 'make streams' test works fine with MPI processes. Thanks, Mikhail
On Thu, Jun 11, 2015 at 4:21 AM, Matthew Knepley <[email protected]> wrote:
On Thu, Jun 11, 2015 at 5:07 AM, Mikhail Khodak < [email protected]> wrote:
Thank you for your help - the install seems to work, apart from routines requiring MPI, which fail due to the "Attempting to use an MPI routine before initializing MPI" error. This seems to be an error in the PETSc build itself.
The MPI routines will not work until after
import petsc4py, sys petsc4py.init(sys.argv) from petsc4py import PETSc
If they fail after this, it is usually a mismatch between the mpiexec being used and the MPI libraries being linked.
Thanks,
Matt
Thanks again,
Mikhail Khodak
On Mon, Jun 8, 2015 at 5:11 AM, Lisandro Dalcin <[email protected]> wrote:
On 8 June 2015 at 02:50, Mikhail Khodak <[email protected]> wrote:
Hello, I am trying to build petsc4py-3.5.1 using Cygwin on 64-bit Windows 7. I have built PETSc 3.5.4 with shared and dynamic libraries using mpich2-1.2.1 and successfully ran the installation tests. I am using Python 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I attempt to install petsc4py (both with pip and distutils) I get a mpicc compiler error due to undefined references/symbols. I have attached the output of running
pip install petsc petsc4py --allow-external petsc --allow-external petsc4py
I've never ever built or test petsc4py under Cygwin. The errors you see are expected. Perhaps you can manually workaround the issues following the following steps:
1) Download the petsc4py tarball and unpack it. 2) Open the file "src/libpetsc4py/libpetsc4py.h", add remove all occurences of DL_IMPORT, i.e, replace DL_IMPORT(XYZ) for just XYZ 3) Use pip again:
pip install petsc pip install .
The last line assumes your current working directory is the one having petsc4py's setup.py
Finally, I do not guarantee this will work. I'm just guessing, petsc4py never explicitly supported Windows and/or Cygwin.
-- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
-- 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 Mikhail, Satish helped me and we managed to get petsc4py working with static builds and Cygwin's Open MPI. Please git pull and try again. On 11 June 2015 at 14:13, Mikhail Khodak <[email protected]> wrote:
I have attached the log files. I tried using Open MPI before but received the same result. I will try a static build later and otherwise will get a VM. Thanks for looking at this, Mikhail
On Thu, Jun 11, 2015 at 10:48 AM, Satish Balay <[email protected]> wrote:
Also - should mention:
- cygwin has OpenMPI pacakged - so you could also try that. - most of my builds are static [so never tried dll builds]
Satish
On Thu, 11 Jun 2015, Satish Balay wrote:
If you get errors when running basic petsc examples - send us the relavant petsc logs [configure.log, make.log, test.log etc..]
Also - note that mpich is not supported on cygwin/windows [it generally works for us - when we try the --download-mpich build].
Unless you really need a cywin build/use of petsc4py - it might be easier to install a linux VM - and use PETSc/petsc4py on it.
Satish
On Thu, 11 Jun 2015, Mikhail Khodak wrote:
I added these lines to the petsc4py test files (specifically test_comm.py) but the error remains the same. However, I have done the standard 'which mpiexec', 'which mpicc', 'which mpirun' and they are all in the same folder. In fact it is the only MPI installed. The reason I thought it might be a PETSc build problem is because one of the PETSc 'make test' tests (ex5f) fails with the same error, even though the 'make streams' test works fine with MPI processes. Thanks, Mikhail
On Thu, Jun 11, 2015 at 4:21 AM, Matthew Knepley <[email protected]> wrote:
On Thu, Jun 11, 2015 at 5:07 AM, Mikhail Khodak <[email protected]> wrote:
Thank you for your help - the install seems to work, apart from routines requiring MPI, which fail due to the "Attempting to use an MPI routine before initializing MPI" error. This seems to be an error in the PETSc build itself.
The MPI routines will not work until after
import petsc4py, sys petsc4py.init(sys.argv) from petsc4py import PETSc
If they fail after this, it is usually a mismatch between the mpiexec being used and the MPI libraries being linked.
Thanks,
Matt
Thanks again,
Mikhail Khodak
On Mon, Jun 8, 2015 at 5:11 AM, Lisandro Dalcin <[email protected]> wrote:
On 8 June 2015 at 02:50, Mikhail Khodak <[email protected]> wrote:
Hello, I am trying to build petsc4py-3.5.1 using Cygwin on 64-bit Windows 7. I have built PETSc 3.5.4 with shared and dynamic libraries using mpich2-1.2.1 and successfully ran the installation tests. I am using Python 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I attempt to install petsc4py (both with pip and distutils) I get a mpicc compiler error due to undefined references/symbols. I have attached the output of running
pip install petsc petsc4py --allow-external petsc --allow-external petsc4py
I've never ever built or test petsc4py under Cygwin. The errors you see are expected. Perhaps you can manually workaround the issues following the following steps:
1) Download the petsc4py tarball and unpack it. 2) Open the file "src/libpetsc4py/libpetsc4py.h", add remove all occurences of DL_IMPORT, i.e, replace DL_IMPORT(XYZ) for just XYZ 3) Use pip again:
pip install petsc pip install .
The last line assumes your current working directory is the one having petsc4py's setup.py
Finally, I do not guarantee this will work. I'm just guessing, petsc4py never explicitly supported Windows and/or Cygwin.
-- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
-- 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
-- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Thank you for reviewing this. The errors for the command 'pip2 install .' inside the petsc4py directory are attached, along with the configure/make logs for the PETSc build. Best, Mikhail Khodak On Mon, Jun 22, 2015 at 12:25 PM, Lisandro Dalcin <[email protected]> wrote:
Dear Mikhail, Satish helped me and we managed to get petsc4py working with static builds and Cygwin's Open MPI. Please git pull and try again.
On 11 June 2015 at 14:13, Mikhail Khodak <[email protected]> wrote:
I have attached the log files. I tried using Open MPI before but received the same result. I will try a static build later and otherwise will get a VM. Thanks for looking at this, Mikhail
On Thu, Jun 11, 2015 at 10:48 AM, Satish Balay <[email protected]> wrote:
Also - should mention:
- cygwin has OpenMPI pacakged - so you could also try that. - most of my builds are static [so never tried dll builds]
Satish
On Thu, 11 Jun 2015, Satish Balay wrote:
If you get errors when running basic petsc examples - send us the relavant petsc logs [configure.log, make.log, test.log etc..]
Also - note that mpich is not supported on cygwin/windows [it generally works for us - when we try the --download-mpich build].
Unless you really need a cywin build/use of petsc4py - it might be easier to install a linux VM - and use PETSc/petsc4py on it.
Satish
On Thu, 11 Jun 2015, Mikhail Khodak wrote:
I added these lines to the petsc4py test files (specifically test_comm.py) but the error remains the same. However, I have done the standard 'which mpiexec', 'which mpicc', 'which mpirun' and they are all in the same folder. In fact it is the only MPI installed. The reason I thought it might be a PETSc build problem is because
one
of the PETSc 'make test' tests (ex5f) fails with the same error, even though the 'make streams' test works fine with MPI processes. Thanks, Mikhail
On Thu, Jun 11, 2015 at 4:21 AM, Matthew Knepley <[email protected]
wrote:
On Thu, Jun 11, 2015 at 5:07 AM, Mikhail Khodak <[email protected]> wrote:
Thank you for your help - the install seems to work, apart from routines requiring MPI, which fail due to the "Attempting to use an MPI routine before initializing MPI" error. This seems to be an error in the PETSc build itself.
The MPI routines will not work until after
import petsc4py, sys petsc4py.init(sys.argv) from petsc4py import PETSc
If they fail after this, it is usually a mismatch between the mpiexec being used and the MPI libraries being linked.
Thanks,
Matt
Thanks again,
Mikhail Khodak
On Mon, Jun 8, 2015 at 5:11 AM, Lisandro Dalcin < [email protected]> wrote:
On 8 June 2015 at 02:50, Mikhail Khodak <[email protected]> wrote:
Hello, I am trying to build petsc4py-3.5.1 using Cygwin on 64-bit Windows 7. I have built PETSc 3.5.4 with shared and dynamic libraries using mpich2-1.2.1 and successfully ran the installation tests. I am using Python 2.7 and NumPy 1.9.2 and have installed mpi4py. However, when I attempt to install petsc4py (both with pip and distutils) I get a mpicc compiler error due to undefined references/symbols. I have attached the output of running
pip install petsc petsc4py --allow-external petsc --allow-external petsc4py
I've never ever built or test petsc4py under Cygwin. The errors you see are expected. Perhaps you can manually workaround the issues following the following steps:
1) Download the petsc4py tarball and unpack it. 2) Open the file "src/libpetsc4py/libpetsc4py.h", add remove all occurences of DL_IMPORT, i.e, replace DL_IMPORT(XYZ) for just XYZ 3) Use pip again:
pip install petsc pip install .
The last line assumes your current working directory is the one having petsc4py's setup.py
Finally, I do not guarantee this will work. I'm just guessing, petsc4py never explicitly supported Windows and/or Cygwin.
-- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
-- 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
-- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
On 23 June 2015 at 12:15, Mikhail Khodak <[email protected]> wrote:
Thank you for reviewing this. The errors for the command 'pip2 install .' inside the petsc4py directory are attached, along with the configure/make logs for the PETSc build. Best, Mikhail Khodak
Not sure what's going on. Do you have PETSC_DIR and PETSC_ARCH in your environment? Does it work if you just do "python setup.py build" ? -- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/ 4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa Office Phone: +966 12 808-0459
Yes, the variables are defined. Using setup.py gives the same error. As a note, I am using a download of the master branch. Mikhail Khodak On Wed, Jun 24, 2015 at 7:15 AM, Lisandro Dalcin <[email protected]> wrote:
On 23 June 2015 at 12:15, Mikhail Khodak <[email protected]> wrote:
Thank you for reviewing this. The errors for the command 'pip2 install .' inside the petsc4py directory are attached, along with the configure/make logs for the PETSc build. Best, Mikhail Khodak
Not sure what's going on.
Do you have PETSC_DIR and PETSC_ARCH in your environment?
Does it work if you just do "python setup.py build" ?
-- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
Perhaps the issue is petsc-3.5. We tried this petsc-3.6 - and that worked fine.. Satish On Wed, 24 Jun 2015, Mikhail Khodak wrote:
Yes, the variables are defined. Using setup.py gives the same error. As a note, I am using a download of the master branch. Mikhail Khodak
On Wed, Jun 24, 2015 at 7:15 AM, Lisandro Dalcin <[email protected]> wrote:
On 23 June 2015 at 12:15, Mikhail Khodak <[email protected]> wrote:
Thank you for reviewing this. The errors for the command 'pip2 install .' inside the petsc4py directory are attached, along with the configure/make logs for the PETSc build. Best, Mikhail Khodak
Not sure what's going on.
Do you have PETSC_DIR and PETSC_ARCH in your environment?
Does it work if you just do "python setup.py build" ?
-- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
That was it. Installed with 3.6.0 and all tests passed. Thank you both for the help. Mikhail Khodak On Wed, Jun 24, 2015 at 7:14 PM, Satish Balay <[email protected]> wrote:
Perhaps the issue is petsc-3.5. We tried this petsc-3.6 - and that worked fine..
Satish
On Wed, 24 Jun 2015, Mikhail Khodak wrote:
Yes, the variables are defined. Using setup.py gives the same error. As a note, I am using a download of the master branch. Mikhail Khodak
On Wed, Jun 24, 2015 at 7:15 AM, Lisandro Dalcin <[email protected]> wrote:
On 23 June 2015 at 12:15, Mikhail Khodak <[email protected]> wrote:
Thank you for reviewing this. The errors for the command 'pip2 install .' inside the petsc4py directory are attached, along with the configure/make logs for the PETSc build. Best, Mikhail Khodak
Not sure what's going on.
Do you have PETSC_DIR and PETSC_ARCH in your environment?
Does it work if you just do "python setup.py build" ?
-- Lisandro Dalcin ============ Research Scientist Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Numerical Porous Media Center (NumPor) King Abdullah University of Science and Technology (KAUST) http://numpor.kaust.edu.sa/
4700 King Abdullah University of Science and Technology al-Khawarizmi Bldg (Bldg 1), Office # 4332 Thuwal 23955-6900, Kingdom of Saudi Arabia http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
participants (4)
-
Lisandro Dalcin -
Matthew Knepley -
Mikhail Khodak -
Satish Balay