Petsc error during mlsvm compilation

[myousefi2016]

I compiled and configured the Petsc with petsc_configure.sh script, which was successfully done. After that I moved to src folder and run the buildAll.sh script to compile the mlsvm, but I got these errors:

[yousefi@node1523 src]$ ./buildAll.sh 
Make all the tools and main application from source code
/home/yousefi/opt/petsc/bin/mpicxx -o etimer.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O  -fPIC    -I/home/yousefi/mlsvm/petsc/include -I/home/yousefi/mlsvm/petsc/linux-no-debug/include -I/home/yousefi/opt/petsc/include   -std=c++11 -g -O3     -w  `pwd`/etimer.cc
/home/yousefi/opt/petsc/bin/mpicxx -o common_funcs.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O  -fPIC    -I/home/yousefi/mlsvm/petsc/include -I/home/yousefi/mlsvm/petsc/linux-no-debug/include -I/home/yousefi/opt/petsc/include   -std=c++11 -g -O3     -w  `pwd`/common_funcs.cc
/home/yousefi/opt/petsc/bin/mpicxx -o loader.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O  -fPIC    -I/home/yousefi/mlsvm/petsc/include -I/home/yousefi/mlsvm/petsc/linux-no-debug/include -I/home/yousefi/opt/petsc/include   -std=c++11 -g -O3     -w  `pwd`/loader.cc
/home/yousefi/opt/petsc/bin/mpicxx -o pugixml.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O  -fPIC    -I/home/yousefi/mlsvm/petsc/include -I/home/yousefi/mlsvm/petsc/linux-no-debug/include -I/home/yousefi/opt/petsc/include   -std=c++11 -g -O3     -w  `pwd`/pugixml.cc
/home/yousefi/opt/petsc/bin/mpicxx -o OptionParser.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O  -fPIC    -I/home/yousefi/mlsvm/petsc/include -I/home/yousefi/mlsvm/petsc/linux-no-debug/include -I/home/yousefi/opt/petsc/include   -std=c++11 -g -O3     -w  `pwd`/OptionParser.cc
/home/yousefi/opt/petsc/bin/mpicxx -o config_params.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O  -fPIC    -I/home/yousefi/mlsvm/petsc/include -I/home/yousefi/mlsvm/petsc/linux-no-debug/include -I/home/yousefi/opt/petsc/include   -std=c++11 -g -O3     -w  `pwd`/config_params.cc
/home/yousefi/opt/petsc/bin/mpicxx -o k_fold.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O  -fPIC    -I/home/yousefi/mlsvm/petsc/include -I/home/yousefi/mlsvm/petsc/linux-no-debug/include -I/home/yousefi/opt/petsc/include   -std=c++11 -g -O3     -w  `pwd`/k_fold.cc
/home/yousefi/mlsvm/src/k_fold.cc: In member function ‘void k_fold::cross_validation_class(int, int, _p_Mat*&, _p_Mat*&, _p_Mat*&, PetscInt*, PetscInt&, std::unordered_set<int>&, std::vector<int>&, const string&, const std::vector<int>&, bool)’:
/home/yousefi/mlsvm/src/k_fold.cc:806:83: error: cannot convert ‘MatReuse’ to ‘_p_Mat**’ for argument ‘4’ to ‘PetscErrorCode MatCreateSubMatrix(Mat, IS, IS, _p_Mat**)’
     MatCreateSubMatrix(m_full_data,is_train, NULL,MAT_INITIAL_MATRIX,&m_train_data);
                                                                                   ^
/home/yousefi/mlsvm/src/k_fold.cc:807:81: error: cannot convert ‘MatReuse’ to ‘_p_Mat**’ for argument ‘4’ to ‘PetscErrorCode MatCreateSubMatrix(Mat, IS, IS, _p_Mat**)’
     MatCreateSubMatrix(m_full_data,is_test, NULL,MAT_INITIAL_MATRIX,&m_test_data);
                                                                                 ^
make: *** [k_fold.o] Error 1
/home/yousefi/opt/petsc/bin/mpicxx -o convertor.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O  -fPIC    -I/home/yousefi/mlsvm/petsc/include -I/home/yousefi/mlsvm/petsc/linux-no-debug/include -I/home/yousefi/opt/petsc/include   -std=c++11 -g -O3     -w  `pwd`/convertor.cc
/home/yousefi/opt/petsc/bin/mpicxx -o k_fold.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O  -fPIC    -I/home/yousefi/mlsvm/petsc/include -I/home/yousefi/mlsvm/petsc/linux-no-debug/include -I/home/yousefi/opt/petsc/include   -std=c++11 -g -O3     -w  `pwd`/k_fold.cc
/home/yousefi/mlsvm/src/k_fold.cc: In member function ‘void k_fold::cross_validation_class(int, int, _p_Mat*&, _p_Mat*&, _p_Mat*&, PetscInt*, PetscInt&, std::unordered_set<int>&, std::vector<int>&, const string&, const std::vector<int>&, bool)’:
/home/yousefi/mlsvm/src/k_fold.cc:806:83: error: cannot convert ‘MatReuse’ to ‘_p_Mat**’ for argument ‘4’ to ‘PetscErrorCode MatCreateSubMatrix(Mat, IS, IS, _p_Mat**)’
     MatCreateSubMatrix(m_full_data,is_train, NULL,MAT_INITIAL_MATRIX,&m_train_data);
                                                                                   ^
/home/yousefi/mlsvm/src/k_fold.cc:807:81: error: cannot convert ‘MatReuse’ to ‘_p_Mat**’ for argument ‘4’ to ‘PetscErrorCode MatCreateSubMatrix(Mat, IS, IS, _p_Mat**)’
     MatCreateSubMatrix(m_full_data,is_test, NULL,MAT_INITIAL_MATRIX,&m_test_data);
                                                                                 ^
make: *** [k_fold.o] Error 1
make: Makefile_palmetto: No such file or directory
make: *** No rule to make target `Makefile_palmetto'.  Stop.
/home/yousefi/opt/petsc/bin/mpicxx -o k_fold.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O  -fPIC    -I/home/yousefi/mlsvm/petsc/include -I/home/yousefi/mlsvm/petsc/linux-no-debug/include -I/home/yousefi/opt/petsc/include   -std=c++11 -g -O3     -w  `pwd`/k_fold.cc
/home/yousefi/mlsvm/src/k_fold.cc: In member function ‘void k_fold::cross_validation_class(int, int, _p_Mat*&, _p_Mat*&, _p_Mat*&, PetscInt*, PetscInt&, std::unordered_set<int>&, std::vector<int>&, const string&, const std::vector<int>&, bool)’:
/home/yousefi/mlsvm/src/k_fold.cc:806:83: error: cannot convert ‘MatReuse’ to ‘_p_Mat**’ for argument ‘4’ to ‘PetscErrorCode MatCreateSubMatrix(Mat, IS, IS, _p_Mat**)’
     MatCreateSubMatrix(m_full_data,is_train, NULL,MAT_INITIAL_MATRIX,&m_train_data);
                                                                                   ^
/home/yousefi/mlsvm/src/k_fold.cc:807:81: error: cannot convert ‘MatReuse’ to ‘_p_Mat**’ for argument ‘4’ to ‘PetscErrorCode MatCreateSubMatrix(Mat, IS, IS, _p_Mat**)’
     MatCreateSubMatrix(m_full_data,is_test, NULL,MAT_INITIAL_MATRIX,&m_test_data);
                                                                                 ^
make: *** [k_fold.o] Error 1
/home/yousefi/opt/petsc/bin/mpicxx -o k_fold.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O  -fPIC    -I/home/yousefi/mlsvm/petsc/include -I/home/yousefi/mlsvm/petsc/linux-no-debug/include -I/home/yousefi/opt/petsc/include   -std=c++11 -g -O3     -w  `pwd`/k_fold.cc
/home/yousefi/mlsvm/src/k_fold.cc: In member function ‘void k_fold::cross_validation_class(int, int, _p_Mat*&, _p_Mat*&, _p_Mat*&, PetscInt*, PetscInt&, std::unordered_set<int>&, std::vector<int>&, const string&, const std::vector<int>&, bool)’:
/home/yousefi/mlsvm/src/k_fold.cc:806:83: error: cannot convert ‘MatReuse’ to ‘_p_Mat**’ for argument ‘4’ to ‘PetscErrorCode MatCreateSubMatrix(Mat, IS, IS, _p_Mat**)’
     MatCreateSubMatrix(m_full_data,is_train, NULL,MAT_INITIAL_MATRIX,&m_train_data);
                                                                                   ^
/home/yousefi/mlsvm/src/k_fold.cc:807:81: error: cannot convert ‘MatReuse’ to ‘_p_Mat**’ for argument ‘4’ to ‘PetscErrorCode MatCreateSubMatrix(Mat, IS, IS, _p_Mat**)’
     MatCreateSubMatrix(m_full_data,is_test, NULL,MAT_INITIAL_MATRIX,&m_test_data);
                                                                                 ^
make: *** [k_fold.o] Error 1
/home/yousefi/opt/petsc/bin/mpicxx -o k_fold.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O  -fPIC    -I/home/yousefi/mlsvm/petsc/include -I/home/yousefi/mlsvm/petsc/linux-no-debug/include -I/home/yousefi/opt/petsc/include   -std=c++11 -g -O3     -w  `pwd`/k_fold.cc
/home/yousefi/mlsvm/src/k_fold.cc: In member function ‘void k_fold::cross_validation_class(int, int, _p_Mat*&, _p_Mat*&, _p_Mat*&, PetscInt*, PetscInt&, std::unordered_set<int>&, std::vector<int>&, const string&, const std::vector<int>&, bool)’:
/home/yousefi/mlsvm/src/k_fold.cc:806:83: error: cannot convert ‘MatReuse’ to ‘_p_Mat**’ for argument ‘4’ to ‘PetscErrorCode MatCreateSubMatrix(Mat, IS, IS, _p_Mat**)’
     MatCreateSubMatrix(m_full_data,is_train, NULL,MAT_INITIAL_MATRIX,&m_train_data);
                                                                                   ^
/home/yousefi/mlsvm/src/k_fold.cc:807:81: error: cannot convert ‘MatReuse’ to ‘_p_Mat**’ for argument ‘4’ to ‘PetscErrorCode MatCreateSubMatrix(Mat, IS, IS, _p_Mat**)’
     MatCreateSubMatrix(m_full_data,is_test, NULL,MAT_INITIAL_MATRIX,&m_test_data);
                                                                                 ^
make: *** [k_fold.o] Error 1
/home/yousefi/opt/petsc/bin/mpicxx -o k_fold.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O  -fPIC    -I/home/yousefi/mlsvm/petsc/include -I/home/yousefi/mlsvm/petsc/linux-no-debug/include -I/home/yousefi/opt/petsc/include   -std=c++11 -g -O3     -w  `pwd`/k_fold.cc
/home/yousefi/mlsvm/src/k_fold.cc: In member function ‘void k_fold::cross_validation_class(int, int, _p_Mat*&, _p_Mat*&, _p_Mat*&, PetscInt*, PetscInt&, std::unordered_set<int>&, std::vector<int>&, const string&, const std::vector<int>&, bool)’:
/home/yousefi/mlsvm/src/k_fold.cc:806:83: error: cannot convert ‘MatReuse’ to ‘_p_Mat**’ for argument ‘4’ to ‘PetscErrorCode MatCreateSubMatrix(Mat, IS, IS, _p_Mat**)’
     MatCreateSubMatrix(m_full_data,is_train, NULL,MAT_INITIAL_MATRIX,&m_train_data);
                                                                                   ^
/home/yousefi/mlsvm/src/k_fold.cc:807:81: error: cannot convert ‘MatReuse’ to ‘_p_Mat**’ for argument ‘4’ to ‘PetscErrorCode MatCreateSubMatrix(Mat, IS, IS, _p_Mat**)’
     MatCreateSubMatrix(m_full_data,is_test, NULL,MAT_INITIAL_MATRIX,&m_test_data);

Any idea how to fix them?

[kspalm]

Are you sure you have the latest version of PETSc properly installed? It looks like its still using version 3.7 if its trying to convert the 4th arg from 'MatReuse' to '_p_Mat**'.

[myousefi2016]

@kspalm I suppose it is the latest version cause I already updated the repo url of PETSc. But, I should say I did not have this problem when I used the PETSc from conda install -c conda-forge petsc which is again version: 3.11.3.

[kspalm]

My only other suggestion is to double check and make sure your $PETSC_DIR and $PETSC_ARCH environment variables point to the correct directories. If they're pointing to the correct ones, then I'm at a loss as to why it would be trying to use the old MatCreateSubMatrix() from 3.7.

[myousefi2016]

My only guess is that you guys used old bitbucket repo of PETSc and I changed it to gitlab repo due to that the bitbucket repo does not exist anymore. Maybe there is an issue with that.