openfpm_pdata issueshttps://git.mpi-cbg.de/mosaic/software/parallel-computing/openfpm/openfpm_pdata/-/issues2023-08-02T16:59:59Zhttps://git.mpi-cbg.de/mosaic/software/parallel-computing/openfpm/openfpm_pdata/-/issues/2Compilation error for PETSC (MacOS Big Sur (11.2.3))2023-08-02T16:59:59ZjstarkCompilation error for PETSC (MacOS Big Sur (11.2.3))Hi,
when using the develop branch, I get the following compilation error:
In file included from /Users/jstark/OPENFPM_DEPENDENCIES_dev/PETSC/include/petscvec.h:9:
In file included from /Users/jstark/OPENFPM_DEPENDENCIES_dev/PETSC/includ...Hi,
when using the develop branch, I get the following compilation error:
In file included from /Users/jstark/OPENFPM_DEPENDENCIES_dev/PETSC/include/petscvec.h:9:
In file included from /Users/jstark/OPENFPM_DEPENDENCIES_dev/PETSC/include/petscis.h:7:
/Users/jstark/OPENFPM_DEPENDENCIES_dev/PETSC/include/petscsys.h:219:6: error: "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version"
# error "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version"
I remember that @Abhinav said he as well had problems with PETSC after updating his mac to Big Sur.
Was it the same issue? And if yes, how did you solve it?Abhinav Singhjstarkfoggiasachin_krishnan_tvAbhinav Singhhttps://git.mpi-cbg.de/mosaic/software/parallel-computing/openfpm/openfpm_pdata/-/issues/3Error when including "DCPSE/DCPSE_op/DCPSE_op.hpp"2023-10-20T16:34:20ZjstarkError when including "DCPSE/DCPSE_op/DCPSE_op.hpp"When including DCPSE_op.hpp (into an otherwise more or less empty main), I get the following compilation error:
In file included from /Users/jstark/Desktop/diffusion/zebrafish/validation_methodOfImages/main.cpp:23:
/Users/jstark/OpenFPM...When including DCPSE_op.hpp (into an otherwise more or less empty main), I get the following compilation error:
In file included from /Users/jstark/Desktop/diffusion/zebrafish/validation_methodOfImages/main.cpp:23:
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:679:18: error: unknown type name 'support_options'; did you mean 'mach_port_options'?
support_options opt = support_options::N_PARTICLES) {
^~~~~~~~~~~~~~~
mach_port_options
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include/mach/port.h:349:16: note: 'mach_port_options' declared here
typedef struct mach_port_options {
^
In file included from /Users/jstark/Desktop/diffusion/zebrafish/validation_methodOfImages/main.cpp:23:
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:694:45: error: use of undeclared identifier 'Dcpse'
vector_dist_expression_op<operand_type, Dcpse<operand_type::vtype::dims, typename operand_type::vtype>, VECT_DCPSE>
^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:694:107: error: expected member name or ';' after declaration specifiers
vector_dist_expression_op<operand_type, Dcpse<operand_type::vtype::dims, typename operand_type::vtype>, VECT_DCPSE>
^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:679:40: error: use of undeclared identifier 'support_options'; did you mean 'mach_port_options'?
support_options opt = support_options::N_PARTICLES) {
^~~~~~~~~~~~~~~
mach_port_options
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include/mach/port.h:349:16: note: 'mach_port_options' declared here
typedef struct mach_port_options {
^
In file included from /Users/jstark/Desktop/diffusion/zebrafish/validation_methodOfImages/main.cpp:23:
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:679:57: error: no member named 'N_PARTICLES' in 'mach_port_options'
support_options opt = support_options::N_PARTICLES) {
~~~~~~~~~~~~~~~~~^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:684:21: error: no template named 'Dcpse'
dcpse = new Dcpse<particles_type::dims, particles_type>(parts, p, ord, rCut, oversampling_factor, opt);
^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:690:43: error: expected ')'
delete (Dcpse<particles_type::dims, particles_type> *) dcpse;
^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:690:16: note: to match this '('
delete (Dcpse<particles_type::dims, particles_type> *) dcpse;
^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:690:63: error: expected ';' after expression
delete (Dcpse<particles_type::dims, particles_type> *) dcpse;
^
;
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:690:17: error: use of undeclared identifier 'Dcpse'; did you mean 'dcpse'?
delete (Dcpse<particles_type::dims, particles_type> *) dcpse;
^~~~~
dcpse
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:661:11: note: 'dcpse' declared here
void *dcpse;
^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:690:64: warning: expression result unused [-Wunused-value]
delete (Dcpse<particles_type::dims, particles_type> *) dcpse;
^~~~~
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:769:18: error: unknown type name 'support_options'; did you mean 'mach_port_options'?
support_options opt = support_options::N_PARTICLES) {
^~~~~~~~~~~~~~~
mach_port_options
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include/mach/port.h:349:16: note: 'mach_port_options' declared here
typedef struct mach_port_options {
^
In file included from /Users/jstark/Desktop/diffusion/zebrafish/validation_methodOfImages/main.cpp:23:
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:790:45: error: use of undeclared identifier 'Dcpse'
vector_dist_expression_op<operand_type, Dcpse<operand_type::vtype::dims, typename operand_type::vtype>, VECT_DCPSE>
^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:790:107: error: expected member name or ';' after declaration specifiers
vector_dist_expression_op<operand_type, Dcpse<operand_type::vtype::dims, typename operand_type::vtype>, VECT_DCPSE>
^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:769:40: error: use of undeclared identifier 'support_options'; did you mean 'mach_port_options'?
support_options opt = support_options::N_PARTICLES) {
^~~~~~~~~~~~~~~
mach_port_options
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include/mach/port.h:349:16: note: 'mach_port_options' declared here
typedef struct mach_port_options {
^
In file included from /Users/jstark/Desktop/diffusion/zebrafish/validation_methodOfImages/main.cpp:23:
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:769:57: error: no member named 'N_PARTICLES' in 'mach_port_options'
support_options opt = support_options::N_PARTICLES) {
~~~~~~~~~~~~~~~~~^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:774:21: error: no template named 'Dcpse'
dcpse = new Dcpse<particles_type::dims, particles_type>(parts, p, ord, rCut, oversampling_factor, opt);
^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:776:9: error: use of undeclared identifier 'Dcpse'; did you mean 'dcpse'?
Dcpse<particles_type::dims, particles_type> *dcpse_ptr = (Dcpse<particles_type::dims, particles_type> *) dcpse;
^~~~~
dcpse
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:750:11: note: 'dcpse' declared here
void *dcpse;
^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:776:9: error: 'dcpse' does not name a template but is followed by template arguments
Dcpse<particles_type::dims, particles_type> *dcpse_ptr = (Dcpse<particles_type::dims, particles_type> *) dcpse;
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:750:11: note: non-template declaration found by name lookup
void *dcpse;
^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:778:13: error: use of undeclared identifier 'dcpse_ptr'
new(dcpse_ptr) Dcpse<particles_type::dims, particles_type>(parts, p, ord, rCut, oversampling_factor, opt);
^
/Users/jstark/OpenFPM_install_dev/openfpm_numerics/include/DCPSE/DCPSE_op/DCPSE_op.hpp:779:9: error: use of undeclared identifier 'dcpse_ptr'
dcpse_ptr++;
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]Abhinav Singhjstarkfoggiasachin_krishnan_tvAbhinav Singhhttps://git.mpi-cbg.de/mosaic/software/parallel-computing/openfpm/openfpm_pdata/-/issues/1Fix installation problems for clang users having OpenMP already installed som...2021-04-27T16:21:44ZjstarkFix installation problems for clang users having OpenMP already installed somewhereIf you have a mac and you are using clang and you have OpenMP already installed somewhere (e.g. because you are using ImageMagick), then you may get a linking error when running make install.
You can fix the problem by helping the comp...If you have a mac and you are using clang and you have OpenMP already installed somewhere (e.g. because you are using ImageMagick), then you may get a linking error when running make install.
You can fix the problem by helping the compiler to find the correct paths by editing openfpm_numerics/src/CMakeLists.txt:
after line 87 add:
target_include_directories (numerics PUBLIC /usr/local/include)
after line 114 add:
target_link_libraries(numerics -L/usr/local/lib -lomp)
(@Pietro: please correct me if this was not formulated well)