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Pysharc Compilation Issue
Hello!
I am having some troulbe installing pysharc. My installation process is as follows:
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Create a conda environment with the following input "conda create -n pysharc_3.0 -c conda-forge python=3.9 numpy scipy h5py six matplotlib python-dateutil pyyaml pyparsing kiwisolver cycler netcdf4 hdf5 h5utils gfortran_linux-64" (This input is directly from the SHARC manual)
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The SHArC program also depends on LAPACK, BLAS, and FFTW, so I add them into my conda environment as well.
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I clone the git repository to an appropriate directory.
-
I add -I and -L flags in the fortran and cc compilers in the Makefile in the source folder.
-
I make the installation in the source directory of SHARC (which does not show errors) and then I use make clean. Then I change use_pysharc in the Makefile to true and cd into the pysharc directory to use make install again.
At this final install, I get a lot of errors about incompatible pointers and any attempt to use the pysharc program fails.
Here is the output I get for both steps:
For the first make install in the source directory, I get: "Updating "build_info.inc" gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c definitions.F90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c matrix.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c string.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c input_list.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c misc.F90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c output.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c decoherence_afssh.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c decoherence_dom.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c nuclear.F90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c electronic.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c qm_out.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c restart.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c qm.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c bsh.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c electronic_laser.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c input.F90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c zpe.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c army_ants.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c tsh_tu.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c pointer_basis.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c driver.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c main.F90 gfortran definitions.o matrix.o string.o input_list.o driver.o misc.o output.o restart.o qm_out.o nuclear.o bsh.o electronic.o qm.o electronic_laser.o input.o decoherence_afssh.o decoherence_dom.o zpe.o tsh_tu.o army_ants.o pointer_basis.o main.o -o sharc1.x -llapack -lfftw3 -lblas -lgfortran ln -sf sharc1.x sharc.x gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c data_extractor.f90 gfortran qm_out.o data_extractor.o definitions.o matrix.o string.o input_list.o -o data_extractor.x -llapack -lfftw3 -lblas -lgfortran gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c diagonalizer.f90 gfortran string.o matrix.o diagonalizer.o -o diagonalizer.x -llapack -lfftw3 -lblas -lgfortran gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c LASER_definitions.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c LASER_calc_fftw.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c LASER_input.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c LASER_main.f90 gfortran LASER_definitions.o LASER_calc_fftw.o LASER_input.o LASER_main.o -o laser.x -llapack -lfftw3 -lblas -lgfortran cp -f *.x ../bin cp -f sharcvars.sh ../bin cp -f sharcvars.csh ../bin"
Then I use make clean and change the use_pysharc variable to true. Then I cd into pysharc and do make install again. This is the output from that:
"(pysharc_3.0) [trscott@login2 pysharc]$ make install
cd netcdf; make lib
make[1]: Entering directory /central/groups/hadtlab/TRS/software/sharc/pysharc/netcdf' gcc -fPIC -I. -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -Wall -c nc_basic.c gcc -fPIC -I. -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -Wall -c nc_sharc.c nc_sharc.c: In function ‘reopen_ncoutputdat’: nc_sharc.c:140:5: warning: passing argument 3 of ‘nc_inq_dimlen’ makes pointer from integer without a cast [enabled by default] check_nccall(iret, ^ In file included from nc_basic.h:28:0, from nc_sharc.h:28, from nc_sharc.c:25: /groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include/netcdf.h:1069:1: note: expected ‘size_t *’ but argument is of type ‘int’ nc_inq_dimlen(int ncid, int dimid, size_t *lenp); ^ nc_sharc.c: In function ‘read_sharc_ncoutputdat_istep_’: nc_sharc.c:301:9: warning: passing argument 3 of ‘nc_inq_dimlen’ from incompatible pointer type [enabled by default] check_nccall(iret, ^ In file included from nc_basic.h:28:0, from nc_sharc.h:28, from nc_sharc.c:25: /groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include/netcdf.h:1069:1: note: expected ‘size_t *’ but argument is of type ‘int *’ nc_inq_dimlen(int ncid, int dimid, size_t *lenp); ^ [ -d ../lib ] || mkdir ../lib ar -cvq ../lib/[libsharcnc.so](http://libsharcnc.so/) nc_basic.o nc_sharc.o a - nc_basic.o a - nc_sharc.o make[1]: Leaving directory /central/groups/hadtlab/TRS/software/sharc/pysharc/netcdf'
cd ../source; make libsharc
make[1]: Entering directory /central/groups/hadtlab/TRS/software/sharc/source' Updating "build_info.inc" gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -D__PYSHARC__ -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c definitions.F90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c matrix.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c string.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c input_list.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -D__PYSHARC__ -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c misc.F90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c output.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c decoherence_afssh.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c decoherence_dom.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -D__PYSHARC__ -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c nuclear.F90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c electronic.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c qm_out.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c restart.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c qm.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c bsh.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c electronic_laser.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -D__PYSHARC__ -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c input.F90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c zpe.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c army_ants.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c tsh_tu.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c pointer_basis.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c driver.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c definitions_NetCDF.f90 gfortran -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -D__PYSHARC__ -O3 -fPIC -g -ffree-line-length-none -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -c interface.F90 gfortran -shared definitions.o matrix.o string.o input_list.o driver.o misc.o output.o restart.o qm_out.o nuclear.o bsh.o electronic.o qm.o electronic_laser.o input.o decoherence_afssh.o decoherence_dom.o zpe.o tsh_tu.o army_ants.o pointer_basis.o interface.o -o ../pysharc/lib/[libsharc.so](http://libsharc.so/) -llapack -lfftw3 -lblas -lgfortran -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -lhdf5 -lhdf5_hl -lmfhdf -ldf -ljpeg -L../pysharc/lib -lsharcnc -lnetcdf make[1]: Leaving directory /central/groups/hadtlab/TRS/software/sharc/source'
python sharc_setup build_ext --build-lib .
running build_ext
building 'sharc/sharc' extension
creating build
creating build/temp.linux-x86_64-cpython-39
creating build/temp.linux-x86_64-cpython-39/pysharc_src
/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -fPIC -O2 -isystem /groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -fPIC -Iinclude -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include/python3.9 -c pysharc_src/pysharc.c -o build/temp.linux-x86_64-cpython-39/pysharc_src/pysharc.o -std=c99 -Wall
In file included from pysharc_src/pysharc.c:338:
pysharc_src/pysharc_QMout.c: In function 'QMout_init':
pysharc_src/pysharc_QMout.c:143:18: warning: passing argument 1 of 'setPointers' from incompatible pointer type [-Wincompatible-pointer-types]
143 | setPointers( (double complex **)H_ptr,
| ^~~~~~~~~~~~~~~~~~~~~~~~
| |
| _Complex double **
In file included from include/libsharc.h:25,
from pysharc_src/pysharc.c:48:
include/interface.h:60:26: note: expected 'void **' but argument is of type '_Complex double **'
60 | void setPointers(void ** H, void ** dm,
| ~~~~~~~~^
pysharc_src/pysharc_QMout.c:144:18: warning: passing argument 2 of 'setPointers' from incompatible pointer type [-Wincompatible-pointer-types]
144 | (double complex **)DM_ptr,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| |
| _Complex double **
include/interface.h:60:37: note: expected 'void **' but argument is of type '_Complex double **'
60 | void setPointers(void ** H, void ** dm,
| ~~~~~~~~^~
pysharc_src/pysharc_QMout.c:145:18: warning: passing argument 3 of 'setPointers' from incompatible pointer type [-Wincompatible-pointer-types]
145 | (double complex **)Ov_ptr,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| |
| _Complex double **
include/interface.h:61:26: note: expected 'void **' but argument is of type '_Complex double **'
61 | void ** overlap,
| ~~~~~~~~^~~~~~~
pysharc_src/pysharc_QMout.c:146:18: warning: passing argument 4 of 'setPointers' from incompatible pointer type [-Wincompatible-pointer-types]
146 | (double **)G_ptr,
| ^~~~~~~~~~~~~~~~
| |
| double **
include/interface.h:62:26: note: expected 'void **' but argument is of type 'double **'
62 | void ** grad,
| ~~~~~~~~^~~~
pysharc_src/pysharc_QMout.c:147:18: warning: passing argument 5 of 'setPointers' from incompatible pointer type [-Wincompatible-pointer-types]
147 | (double **)NACDR_ptr);
| ^~~~~~~~~~~~~~~~~~~~
| |
| double **
include/interface.h:63:26: note: expected 'void **' but argument is of type 'double **'
63 | void ** nacs
| ~~~~~~~~^~~~
In file included from pysharc_src/pysharc.c:340:
pysharc_src/pysharc_QMin.c: In function 'QMin_new':
pysharc_src/pysharc_QMin.c:55:10: warning: assignment to 'QMin *' from incompatible pointer type 'QMout ' [-Wincompatible-pointer-types]
55 | self = (QMout )type->tp_alloc(type, 0);
| ^
pysharc_src/pysharc_QMin.c: In function 'QMin_init':
pysharc_src/pysharc_QMin.c:77:22: warning: passing argument 1 of 'setQMinPointers' from incompatible pointer type [-Wincompatible-pointer-types]
77 | setQMinPointers( (double **)Crd_ptr );
| ^~~~~~~~~~~~~~~~~~
| |
| double **
include/interface.h:65:30: note: expected 'void **' but argument is of type 'double **'
65 | void setQMinPointers(void ** Crd);
| ~~~~~~~~^~~
pysharc_src/pysharc_QMout.c: In function 'QMout_set_nacdr':
pysharc_src/pysharc_QMout.c:512:9: warning: 'state_state_nac' may be used uninitialized [-Wmaybe-uninitialized]
512 | free(state_state_nac);
| ^~~~~~~~~~~~~~~~~~~~~
pysharc_src/pysharc_QMout.c:459:14: note: 'state_state_nac' was declared here
459 | double * state_state_nac;
| ^~~~~~~~~~~~~~~
pysharc_src/pysharc_QMout.c: In function 'QMout_set_gradient':
pysharc_src/pysharc_QMout.c:304:9: warning: 'state_gradient' may be used uninitialized [-Wmaybe-uninitialized]
304 | free(state_gradient);
| ^~~~~~~~~~~~~~~~~~~~
pysharc_src/pysharc_QMout.c:256:14: note: 'state_gradient' was declared here
256 | double * state_gradient;
| ^~~~~~~~~~~~~~
/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -fPIC -O2 -isystem /groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -fPIC -Iinclude -I/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include/python3.9 -c pysharc_src/pysharc_tools.c -o build/temp.linux-x86_64-cpython-39/pysharc_src/pysharc_tools.o -std=c99 -Wall
/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/bin/x86_64-conda-linux-gnu-cc -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -Wl,-rpath-link,/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -Wl,-rpath-link,/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -Wl,-rpath-link,/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -L/groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/hadtlab/TRS/miniconda/envs/pysharc_3.0/include build/temp.linux-x86_64-cpython-39/pysharc_src/pysharc.o build/temp.linux-x86_64-cpython-39/pysharc_src/pysharc_tools.o -Llib -L$ANACONDA/lib -lsharc -o ./sharc/sharc.cpython-39-x86_64-linux-gnu.so
cp lib/.so ../lib
cp bin/.py ../bin"
Please let me know if you need any other information from me about my compilation steps or other outputs. Thanks for your time!
Best, Thais
