Compiling issue

[sachiwee]

Hello, I get the following error while trying to compile. Could you please help me? Thank you very much!

./scripts/build/codeDirectivesParse.pl pwd Use of uninitialized value $ENV{"GALACTICUS_EXEC_PATH"} in concatenation (.) or string at ./scripts/build/codeDirectivesParse.pl line 5. Can't locate File/Changes.pm in @INC (you may need to install the File::Changes module) (@INC contains: /perl /opt/local/lib/perl5/site_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.28 /opt/local/lib/perl5/vendor_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.28 /opt/local/lib/perl5/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/5.28) at ./scripts/build/codeDirectivesParse.pl line 9. BEGIN failed--compilation aborted at ./scripts/build/codeDirectivesParse.pl line 9. gfortran source/hdf5FCInterop.F90 -o ./work/build/hdf5FCInterop.exe -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /usr/local/finclude -fintrinsic-modules-path /usr/local/include/gfortran -fintrinsic-modules-path /usr/local/include -fintrinsic-modules-path /usr/lib/gfortran/modules -fintrinsic-modules-path /usr/include/gfortran -fintrinsic-modules-path /usr/include -fintrinsic-modules-path /usr/finclude -fintrinsic-modules-path /usr/lib64/gfortran/modules -fintrinsic-modules-path /usr/lib64/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -g -DOFDUNAVAIL -DFFTW3UNAVAIL -DANNUNAVAIL -DMATHEVALUNAVAIL source/hdf5FCInterop.F90:28:20:

28 | use :: HDF5 , only : hid_t, hsize_t, size_t | 1 Fatal Error: Cannot open module file 'hdf5.mod' for reading at (1): No such file or directory compilation terminated. make: *** [work/build/hdf5FCInterop.exe] Error 1

[abensonca]

The first error I see is that GALACTICUS_EXEC_PATH is undefined.

You should set this to the path where you're compiling Galacticus. For example, if you're already in that directory you can just do:

export GALACTICUS_EXEC_PATH=`pwd`

Then you should clear out the failed build:

rm -rf work/build

and then try compiling again.

If you run into more problems post the error messages here and I'll try to help.

[sachiwee]

I tried that. But still get the same error

[abensonca]

The other error on your original report showed:

Fatal Error: Cannot open module file 'hdf5.mod' for reading at (1): No such file or directory
compilation terminated.

which means it can't find the HDF5.mod file. Have you already installed the HDF5 library? If you have then you may just need to set the path to it. You can do this by adding

-fintrinsic-modules-path /path/to/install/include

where /path/to/install is the path where you installed HDF5.

[sachiwee]

There is some progress. A different error this time

./scripts/build/findExecutables.pl pwd Use of uninitialized value $ENV{"GALACTICUS_EXEC_PATH"} in concatenation (.) or string at ./scripts/build/findExecutables.pl line 6. ./scripts/build/codeDirectivesParse.pl pwd Use of uninitialized value $ENV{"GALACTICUS_EXEC_PATH"} in concatenation (.) or string at ./scripts/build/codeDirectivesParse.pl line 5. Can't locate File/Changes.pm in @INC (you may need to install the File::Changes module) (@INC contains: /perl /opt/local/lib/perl5/site_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.28 /opt/local/lib/perl5/vendor_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.28 /opt/local/lib/perl5/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/5.28) at ./scripts/build/codeDirectivesParse.pl line 9. BEGIN failed--compilation aborted at ./scripts/build/codeDirectivesParse.pl line 9. ./scripts/build/includeDependencies.pl pwd Use of uninitialized value $ENV{"GALACTICUS_EXEC_PATH"} in concatenation (.) or string at ./scripts/build/includeDependencies.pl line 5. /opt/local/bin/g++ -c source/libmatheval_config.cpp -o ./work/build/libmatheval_config.o -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -g -DOFDLOCKS > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DMATHEVALAVAIL" > ./work/build/Makefile_Config_MathEval ; \ echo "CPPFLAGS += -DMATHEVALAVAIL" >> ./work/build/Makefile_Config_MathEval ; \ else \ echo "FCFLAGS += -DMATHEVALUNAVAIL" > ./work/build/Makefile_Config_MathEval ; \ echo "CPPFLAGS += -DMATHEVALUNAVAIL" >> ./work/build/Makefile_Config_MathEval ; \ fi /opt/local/bin/g++ -c source/ann_config.cpp -o ./work/build/ann_config.o -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -g -DOFDLOCKS > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DANNAVAIL" > ./work/build/Makefile_Config_ANN ; \ echo "CPPFLAGS += -DANNAVAIL" >> ./work/build/Makefile_Config_ANN ; \ else \ echo "FCFLAGS += -DANNUNAVAIL" > ./work/build/Makefile_Config_ANN ; \ echo "CPPFLAGS += -DANNUNAVAIL" >> ./work/build/Makefile_Config_ANN ; \ fi /opt/local/bin/gfortran -c source/fftw3_config.F90 -o ./work/build/fftw3_config.o -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/lib/gfortran/modules -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran/modules -fintrinsic-modules-path /opt/local/bin/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -fintrinsic-modules-path /usr/local/bin/include -g > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DFFTW3AVAIL" > ./work/build/Makefile_Config_FFTW3 ; \ else \ echo "FCFLAGS += -DFFTW3UNAVAIL" > ./work/build/Makefile_Config_FFTW3 ; \ fi /opt/local/bin/gcc -c source/flock_config.c -o ./work/build/flock_config.o -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -g -DOFDLOCKS > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DOFDAVAIL" > ./work/build/Makefile_Config_OFD ; \ echo "CFLAGS += -DOFDAVAIL" >> ./work/build/Makefile_Config_OFD ; \ echo "CPPFLAGS += -DOFDAVAIL" >> ./work/build/Makefile_Config_OFD ; \ else \ echo "FCFLAGS += -DOFDUNAVAIL" > ./work/build/Makefile_Config_OFD ; \ echo "CFLAGS += -DOFDUNAVAIL" >> ./work/build/Makefile_Config_OFD ; \ echo "CPPFLAGS += -DOFDUNAVAIL" >> ./work/build/Makefile_Config_OFD ; \ fi ./scripts/build/codeDirectivesParse.pl pwd Use of uninitialized value $ENV{"GALACTICUS_EXEC_PATH"} in concatenation (.) or string at ./scripts/build/codeDirectivesParse.pl line 5. Can't locate File/Changes.pm in @INC (you may need to install the File::Changes module) (@INC contains: /perl /opt/local/lib/perl5/site_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.28 /opt/local/lib/perl5/vendor_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.28 /opt/local/lib/perl5/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/5.28) at ./scripts/build/codeDirectivesParse.pl line 9. BEGIN failed--compilation aborted at ./scripts/build/codeDirectivesParse.pl line 9. /opt/local/bin/gfortran source/hdf5FCInterop.F90 -o ./work/build/hdf5FCInterop.exe -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/lib/gfortran/modules -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran/modules -fintrinsic-modules-path /opt/local/bin/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -fintrinsic-modules-path /usr/local/bin/include -g -DOFDUNAVAIL -DFFTW3UNAVAIL -DANNUNAVAIL -DMATHEVALUNAVAIL /opt/local/bin/gcc source/hdf5FCInteropC.c -o ./work/build/hdf5FCInteropC.exe -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -g -DOFDLOCKS -DOFDUNAVAIL source/hdf5FCInteropC.c:3:10: fatal error: H5Tpublic.h: No such file or directory 3 | #include "H5Tpublic.h" | ^~~~~ compilation terminated.

[abensonca]

It looks like you still need to set GALACTICUS_EXEC_PATH - did you try setting it using:

export GALACTICUS_EXEC_PATH=`pwd`

before you try compiling?

Also, it's missing further include paths. Try the following. First set INSTALL_PATH to the path where you installed libraries (such as hdf5):

export INSTALL_PATH=/path/to/my/install

and then do:

export GALACTICUS_FCFLAGS="-fintrinsic-modules-path $INSTALL_PATH/finclude -fintrinsic-modules-path $INSTALL_PATH/include -fintrinsic-modules-path $INSTALL_PATH/include/gfortran -fintrinsic-modules-path $INSTALL_PATH/lib/gfortran/modules -L$INSTALL_PATH/lib -L$INSTALL_PATH/lib64"
export GALACTICUS_CFLAGS="-I$INSTALL_PATH/include"
export GALACTICUS_CPPFLAGS="-I$INSTALL_PATH/include"

If that doesn't solve the compilation problem let me know.

[sachiwee]

I have some of them in /opt/local/bin and some in /usr/local/bin how do I set the path in this situation?

[abensonca]

Try:

export INSTALL_PATH1=/opt/local/bin
export INSTALL_PATH2=/usr/local/bin
export GALACTICUS_FCFLAGS="-fintrinsic-modules-path $INSTALL_PATH1/finclude -fintrinsic-modules-path $INSTALL_PATH1/include -fintrinsic-modules-path $INSTALL_PATH1/include/gfortran -fintrinsic-modules-path $INSTALL_PATH1/lib/gfortran/modules -L$INSTALL_PATH1/lib -L$INSTALL_PATH1/lib64 -fintrinsic-modules-path $INSTALL_PATH2/finclude -fintrinsic-modules-path $INSTALL_PATH2/include -fintrinsic-modules-path $INSTALL_PATH2/include/gfortran -fintrinsic-modules-path $INSTALL_PATH2/lib/gfortran/modules -L$INSTALL_PATH2/lib -L$INSTALL_PATH2/lib64"
export GALACTICUS_CFLAGS="-I$INSTALL_PATH1/include -I$INSTALL_PATH2/include"
export GALACTICUS_CPPFLAGS="-I$INSTALL_PATH1/include -I$INSTALL_PATH2/include"

[sachiwee]

Tried that but I still get the same error

[abensonca]

Can you post the full output?

[sachiwee]

NABOO:galacticus sachi.wee$ sudo rm -rf work/build NABOO:galacticus sachi.wee$ export GALACTICUS_EXEC_PATH=pwd NABOO:galacticus sachi.wee$ export INSTALL_PATH1=/opt/local/bin NABOO:galacticus sachi.wee$ export INSTALL_PATH2=/usr/local/bin NABOO:galacticus sachi.wee$ export GALACTICUS_FCFLAGS="-fintrinsic-modules-path $INSTALL_PATH1/finclude -fintrinsic-modules-path $INSTALL_PATH1/include -fintrinsic-modules-path $INSTALL_PATH1/include/gfortran -fintrinsic-modules-path $INSTALL_PATH1/lib/gfortran/modules -L$INSTALL_PATH1/lib -L$INSTALL_PATH1/lib64 -fintrinsic-modules-path $INSTALL_PATH2/finclude -fintrinsic-modules-path $INSTALL_PATH2/include -fintrinsic-modules-path $INSTALL_PATH2/include/gfortran -fintrinsic-modules-path $INSTALL_PATH2/lib/gfortran/modules -L$INSTALL_PATH2/lib -L$INSTALL_PATH2/lib64" NABOO:galacticus sachi.wee$ export GALACTICUS_CFLAGS="-I$INSTALL_PATH1/include -I$INSTALL_PATH2/include" NABOO:galacticus sachi.wee$ export GALACTICUS_CPPFLAGS="-I$INSTALL_PATH1/include -I$INSTALL_PATH2/include" NABOO:galacticus sachi.wee$ sudo make Galacticus.exe ./scripts/build/findExecutables.pl pwd Use of uninitialized value $ENV{"GALACTICUS_EXEC_PATH"} in concatenation (.) or string at ./scripts/build/findExecutables.pl line 6. ./scripts/build/codeDirectivesParse.pl pwd Use of uninitialized value $ENV{"GALACTICUS_EXEC_PATH"} in concatenation (.) or string at ./scripts/build/codeDirectivesParse.pl line 5. Can't locate File/Changes.pm in @INC (you may need to install the File::Changes module) (@INC contains: /perl /opt/local/lib/perl5/site_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.28 /opt/local/lib/perl5/vendor_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.28 /opt/local/lib/perl5/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/5.28) at ./scripts/build/codeDirectivesParse.pl line 9. BEGIN failed--compilation aborted at ./scripts/build/codeDirectivesParse.pl line 9. ./scripts/build/includeDependencies.pl pwd Use of uninitialized value $ENV{"GALACTICUS_EXEC_PATH"} in concatenation (.) or string at ./scripts/build/includeDependencies.pl line 5. /opt/local/bin/g++ -c source/libmatheval_config.cpp -o ./work/build/libmatheval_config.o -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -g -DOFDLOCKS > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DMATHEVALAVAIL" > ./work/build/Makefile_Config_MathEval ; \ echo "CPPFLAGS += -DMATHEVALAVAIL" >> ./work/build/Makefile_Config_MathEval ; \ else \ echo "FCFLAGS += -DMATHEVALUNAVAIL" > ./work/build/Makefile_Config_MathEval ; \ echo "CPPFLAGS += -DMATHEVALUNAVAIL" >> ./work/build/Makefile_Config_MathEval ; \ fi /opt/local/bin/g++ -c source/ann_config.cpp -o ./work/build/ann_config.o -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -g -DOFDLOCKS > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DANNAVAIL" > ./work/build/Makefile_Config_ANN ; \ echo "CPPFLAGS += -DANNAVAIL" >> ./work/build/Makefile_Config_ANN ; \ else \ echo "FCFLAGS += -DANNUNAVAIL" > ./work/build/Makefile_Config_ANN ; \ echo "CPPFLAGS += -DANNUNAVAIL" >> ./work/build/Makefile_Config_ANN ; \ fi /opt/local/bin/gfortran -c source/fftw3_config.F90 -o ./work/build/fftw3_config.o -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/lib/gfortran/modules -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran/modules -fintrinsic-modules-path /opt/local/bin/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -fintrinsic-modules-path /usr/local/bin/include -g > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DFFTW3AVAIL" > ./work/build/Makefile_Config_FFTW3 ; \ else \ echo "FCFLAGS += -DFFTW3UNAVAIL" > ./work/build/Makefile_Config_FFTW3 ; \ fi /opt/local/bin/gcc -c source/flock_config.c -o ./work/build/flock_config.o -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -g -DOFDLOCKS > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DOFDAVAIL" > ./work/build/Makefile_Config_OFD ; \ echo "CFLAGS += -DOFDAVAIL" >> ./work/build/Makefile_Config_OFD ; \ echo "CPPFLAGS += -DOFDAVAIL" >> ./work/build/Makefile_Config_OFD ; \ else \ echo "FCFLAGS += -DOFDUNAVAIL" > ./work/build/Makefile_Config_OFD ; \ echo "CFLAGS += -DOFDUNAVAIL" >> ./work/build/Makefile_Config_OFD ; \ echo "CPPFLAGS += -DOFDUNAVAIL" >> ./work/build/Makefile_Config_OFD ; \ fi ./scripts/build/codeDirectivesParse.pl pwd Use of uninitialized value $ENV{"GALACTICUS_EXEC_PATH"} in concatenation (.) or string at ./scripts/build/codeDirectivesParse.pl line 5. Can't locate File/Changes.pm in @INC (you may need to install the File::Changes module) (@INC contains: /perl /opt/local/lib/perl5/site_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.28 /opt/local/lib/perl5/vendor_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.28 /opt/local/lib/perl5/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/5.28) at ./scripts/build/codeDirectivesParse.pl line 9. BEGIN failed--compilation aborted at ./scripts/build/codeDirectivesParse.pl line 9. /opt/local/bin/gfortran source/hdf5FCInterop.F90 -o ./work/build/hdf5FCInterop.exe -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/lib/gfortran/modules -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran/modules -fintrinsic-modules-path /opt/local/bin/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -fintrinsic-modules-path /usr/local/bin/include -g -DOFDUNAVAIL -DFFTW3UNAVAIL -DANNUNAVAIL -DMATHEVALUNAVAIL /opt/local/bin/gcc source/hdf5FCInteropC.c -o ./work/build/hdf5FCInteropC.exe -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -g -DOFDLOCKS -DOFDUNAVAIL source/hdf5FCInteropC.c:3:10: fatal error: H5Tpublic.h: No such file or directory 3 | #include "H5Tpublic.h" | ^~~~~ compilation terminated. make: *** [work/build/hdf5FCInteropC.exe] Error 1 NABOO:galacticus sachi.wee$

[abensonca]

It may be because you're running make as sudo. I'd suggest putting all of the commands into a script, called buildGalacticus.sh like this:

#!/bin/sh
export GALACTICUS_EXEC_PATH=pwd
export INSTALL_PATH1=/opt/local/bin
export INSTALL_PATH2=/usr/local/bin
export GALACTICUS_FCFLAGS="-fintrinsic-modules-path $INSTALL_PATH1/finclude -fintrinsic-modules-path $INSTALL_PATH1/include -fintrinsic-modules-path $INSTALL_PATH1/include/gfortran -fintrinsic-modules-path $INSTALL_PATH1/lib/gfortran/modules -L$INSTALL_PATH1/lib -L$INSTALL_PATH1/lib64 -fintrinsic-modules-path $INSTALL_PATH2/finclude -fintrinsic-modules-path $INSTALL_PATH2/include -fintrinsic-modules-path $INSTALL_PATH2/include/gfortran -fintrinsic-modules-path $INSTALL_PATH2/lib/gfortran/modules -L$INSTALL_PATH2/lib -L$INSTALL_PATH2/lib64"
export GALACTICUS_CFLAGS="-I$INSTALL_PATH1/include -I$INSTALL_PATH2/include"
export GALACTICUS_CPPFLAGS="-I$INSTALL_PATH1/include -I$INSTALL_PATH2/include"
make Galacticus.exe

make the script executable:

chmod u=wrx buildGalacticus.sh

and then run the script as sudo:

sudo ./buildGalacticus.sh

and see if that works.

[sachiwee]

Some progress. A different error this time. But lib64 doesn't exist in either of the paths

sudo ./buildGalacticus.sh ./scripts/build/findExecutables.pl pwd ./scripts/build/codeDirectivesParse.pl pwd Can't locate File/Changes.pm in @INC (you may need to install the File::Changes module) (@INC contains: pwd/perl /opt/local/lib/perl5/site_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.28 /opt/local/lib/perl5/vendor_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.28 /opt/local/lib/perl5/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/5.28) at ./scripts/build/codeDirectivesParse.pl line 9. BEGIN failed--compilation aborted at ./scripts/build/codeDirectivesParse.pl line 9. ./scripts/build/includeDependencies.pl pwd /opt/local/bin/g++ -c source/libmatheval_config.cpp -o ./work/build/libmatheval_config.o -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -I/opt/local/bin/include -I/usr/local/bin/include -g -DOFDLOCKS > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DMATHEVALAVAIL" > ./work/build/Makefile_Config_MathEval ; \ echo "CPPFLAGS += -DMATHEVALAVAIL" >> ./work/build/Makefile_Config_MathEval ; \ else \ echo "FCFLAGS += -DMATHEVALUNAVAIL" > ./work/build/Makefile_Config_MathEval ; \ echo "CPPFLAGS += -DMATHEVALUNAVAIL" >> ./work/build/Makefile_Config_MathEval ; \ fi /opt/local/bin/g++ -c source/ann_config.cpp -o ./work/build/ann_config.o -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -I/opt/local/bin/include -I/usr/local/bin/include -g -DOFDLOCKS > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DANNAVAIL" > ./work/build/Makefile_Config_ANN ; \ echo "CPPFLAGS += -DANNAVAIL" >> ./work/build/Makefile_Config_ANN ; \ else \ echo "FCFLAGS += -DANNUNAVAIL" > ./work/build/Makefile_Config_ANN ; \ echo "CPPFLAGS += -DANNUNAVAIL" >> ./work/build/Makefile_Config_ANN ; \ fi /opt/local/bin/gfortran -c source/fftw3_config.F90 -o ./work/build/fftw3_config.o -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/bin/finclude -fintrinsic-modules-path /opt/local/bin/include -fintrinsic-modules-path /opt/local/bin/include/gfortran -fintrinsic-modules-path /opt/local/bin/lib/gfortran/modules -L/opt/local/bin/lib -L/opt/local/bin/lib64 -fintrinsic-modules-path /usr/local/bin/finclude -fintrinsic-modules-path /usr/local/bin/include -fintrinsic-modules-path /usr/local/bin/include/gfortran -fintrinsic-modules-path /usr/local/bin/lib/gfortran/modules -L/usr/local/bin/lib -L/usr/local/bin/lib64 -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/lib/gfortran/modules -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran/modules -fintrinsic-modules-path /opt/local/bin/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -fintrinsic-modules-path /usr/local/bin/include -g > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DFFTW3AVAIL" > ./work/build/Makefile_Config_FFTW3 ; \ else \ echo "FCFLAGS += -DFFTW3UNAVAIL" > ./work/build/Makefile_Config_FFTW3 ; \ fi /opt/local/bin/gcc -c source/flock_config.c -o ./work/build/flock_config.o -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -I/opt/local/bin/include -I/usr/local/bin/include -g -DOFDLOCKS > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DOFDAVAIL" > ./work/build/Makefile_Config_OFD ; \ echo "CFLAGS += -DOFDAVAIL" >> ./work/build/Makefile_Config_OFD ; \ echo "CPPFLAGS += -DOFDAVAIL" >> ./work/build/Makefile_Config_OFD ; \ else \ echo "FCFLAGS += -DOFDUNAVAIL" > ./work/build/Makefile_Config_OFD ; \ echo "CFLAGS += -DOFDUNAVAIL" >> ./work/build/Makefile_Config_OFD ; \ echo "CPPFLAGS += -DOFDUNAVAIL" >> ./work/build/Makefile_Config_OFD ; \ fi ./scripts/build/codeDirectivesParse.pl pwd Can't locate File/Changes.pm in @INC (you may need to install the File::Changes module) (@INC contains: pwd/perl /opt/local/lib/perl5/site_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.28 /opt/local/lib/perl5/vendor_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.28 /opt/local/lib/perl5/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/5.28) at ./scripts/build/codeDirectivesParse.pl line 9. BEGIN failed--compilation aborted at ./scripts/build/codeDirectivesParse.pl line 9. /opt/local/bin/gfortran source/hdf5FCInterop.F90 -o ./work/build/hdf5FCInterop.exe -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/bin/finclude -fintrinsic-modules-path /opt/local/bin/include -fintrinsic-modules-path /opt/local/bin/include/gfortran -fintrinsic-modules-path /opt/local/bin/lib/gfortran/modules -L/opt/local/bin/lib -L/opt/local/bin/lib64 -fintrinsic-modules-path /usr/local/bin/finclude -fintrinsic-modules-path /usr/local/bin/include -fintrinsic-modules-path /usr/local/bin/include/gfortran -fintrinsic-modules-path /usr/local/bin/lib/gfortran/modules -L/usr/local/bin/lib -L/usr/local/bin/lib64 -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/lib/gfortran/modules -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran/modules -fintrinsic-modules-path /opt/local/bin/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -fintrinsic-modules-path /usr/local/bin/include -g -DOFDUNAVAIL -DFFTW3UNAVAIL -DANNUNAVAIL -DMATHEVALUNAVAIL ld: warning: directory not found for option '-L/opt/local/bin/lib64' ld: warning: directory not found for option '-L/usr/local/bin/lib64' /opt/local/bin/gcc source/hdf5FCInteropC.c -o ./work/build/hdf5FCInteropC.exe -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -I/opt/local/bin/include -I/usr/local/bin/include -g -DOFDLOCKS -DOFDUNAVAIL ./work/build/hdf5FCInterop.exe > ./work/build/hdf5FCInterop.dat ./work/build/hdf5FCInteropC.exe >> ./work/build/hdf5FCInterop.dat ./scripts/build/enumerateOpenMPCriticalSections.pl pwd Can't locate Fortran/Utils.pm in @INC (you may need to install the Fortran::Utils module) (@INC contains: pwd/perl /opt/local/lib/perl5/site_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.28 /opt/local/lib/perl5/vendor_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.28 /opt/local/lib/perl5/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/5.28) at ./scripts/build/enumerateOpenMPCriticalSections.pl line 7. BEGIN failed--compilation aborted at ./scripts/build/enumerateOpenMPCriticalSections.pl line 7. make: *** [work/build/openMPCriticalSections.xml] Error 2

[abensonca]

It looks like your command to set GALACTICUS_EXEC_PATH isn't working as intended - it needs to be:

export GALACTICUS_EXEC_PATH=`pwd`

using backticks, not single quotes.

Alternatively, just use pwd to show you the current path where you're building Galacticus, and then change the command in your script to:

export GALACTICUS_EXEC_PATH=XYZ

replaceing XYZ with the output from the pwd command.

[sachiwee]

Now I get this error. But I have Sort::Topological installed

sudo ./buildGalacticus.sh ./scripts/build/findExecutables.pl pwd ./scripts/build/codeDirectivesParse.pl pwd ./scripts/build/stateStorables.pl pwd Can't locate Sort/Topological.pm in @INC (you may need to install the Sort::Topological module) (@INC contains: /Users/sachi.wee/galacticus/perl /opt/local/lib/perl5/site_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.28 /opt/local/lib/perl5/vendor_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.28 /opt/local/lib/perl5/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/5.28) at /Users/sachi.wee/galacticus/perl/Galacticus/Build/SourceTree/Process/FunctionClass.pm line 11. BEGIN failed--compilation aborted at /Users/sachi.wee/galacticus/perl/Galacticus/Build/SourceTree/Process/FunctionClass.pm line 11. Compilation failed in require at /Users/sachi.wee/galacticus/perl/Galacticus/Build/SourceTree.pm line 21. BEGIN failed--compilation aborted at /Users/sachi.wee/galacticus/perl/Galacticus/Build/SourceTree.pm line 21. Compilation failed in require at ./scripts/build/stateStorables.pl line 8. BEGIN failed--compilation aborted at ./scripts/build/stateStorables.pl line 8. ./scripts/build/includeDependencies.pl pwd /opt/local/bin/g++ -c source/libmatheval_config.cpp -o ./work/build/libmatheval_config.o -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -I/opt/local/bin/include -I/usr/local/bin/include -g -DOFDLOCKS > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DMATHEVALAVAIL" > ./work/build/Makefile_Config_MathEval ; \ echo "CPPFLAGS += -DMATHEVALAVAIL" >> ./work/build/Makefile_Config_MathEval ; \ else \ echo "FCFLAGS += -DMATHEVALUNAVAIL" > ./work/build/Makefile_Config_MathEval ; \ echo "CPPFLAGS += -DMATHEVALUNAVAIL" >> ./work/build/Makefile_Config_MathEval ; \ fi /opt/local/bin/g++ -c source/ann_config.cpp -o ./work/build/ann_config.o -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -I/opt/local/bin/include -I/usr/local/bin/include -g -DOFDLOCKS > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DANNAVAIL" > ./work/build/Makefile_Config_ANN ; \ echo "CPPFLAGS += -DANNAVAIL" >> ./work/build/Makefile_Config_ANN ; \ else \ echo "FCFLAGS += -DANNUNAVAIL" > ./work/build/Makefile_Config_ANN ; \ echo "CPPFLAGS += -DANNUNAVAIL" >> ./work/build/Makefile_Config_ANN ; \ fi /opt/local/bin/gfortran -c source/fftw3_config.F90 -o ./work/build/fftw3_config.o -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/bin/finclude -fintrinsic-modules-path /opt/local/bin/include -fintrinsic-modules-path /opt/local/bin/include/gfortran -fintrinsic-modules-path /opt/local/bin/lib/gfortran/modules -L/opt/local/bin/lib -L/opt/local/bin/lib64 -fintrinsic-modules-path /usr/local/bin/finclude -fintrinsic-modules-path /usr/local/bin/include -fintrinsic-modules-path /usr/local/bin/include/gfortran -fintrinsic-modules-path /usr/local/bin/lib/gfortran/modules -L/usr/local/bin/lib -L/usr/local/bin/lib64 -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/lib/gfortran/modules -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran/modules -fintrinsic-modules-path /opt/local/bin/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -fintrinsic-modules-path /usr/local/bin/include -g > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DFFTW3AVAIL" > ./work/build/Makefile_Config_FFTW3 ; \ else \ echo "FCFLAGS += -DFFTW3UNAVAIL" > ./work/build/Makefile_Config_FFTW3 ; \ fi /opt/local/bin/gcc -c source/flock_config.c -o ./work/build/flock_config.o -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -I/opt/local/bin/include -I/usr/local/bin/include -g -DOFDLOCKS > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DOFDAVAIL" > ./work/build/Makefile_Config_OFD ; \ echo "CFLAGS += -DOFDAVAIL" >> ./work/build/Makefile_Config_OFD ; \ echo "CPPFLAGS += -DOFDAVAIL" >> ./work/build/Makefile_Config_OFD ; \ else \ echo "FCFLAGS += -DOFDUNAVAIL" > ./work/build/Makefile_Config_OFD ; \ echo "CFLAGS += -DOFDUNAVAIL" >> ./work/build/Makefile_Config_OFD ; \ echo "CPPFLAGS += -DOFDUNAVAIL" >> ./work/build/Makefile_Config_OFD ; \ fi /opt/local/bin/gfortran source/hdf5FCInterop.F90 -o ./work/build/hdf5FCInterop.exe -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/bin/finclude -fintrinsic-modules-path /opt/local/bin/include -fintrinsic-modules-path /opt/local/bin/include/gfortran -fintrinsic-modules-path /opt/local/bin/lib/gfortran/modules -L/opt/local/bin/lib -L/opt/local/bin/lib64 -fintrinsic-modules-path /usr/local/bin/finclude -fintrinsic-modules-path /usr/local/bin/include -fintrinsic-modules-path /usr/local/bin/include/gfortran -fintrinsic-modules-path /usr/local/bin/lib/gfortran/modules -L/usr/local/bin/lib -L/usr/local/bin/lib64 -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/lib/gfortran/modules -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran/modules -fintrinsic-modules-path /opt/local/bin/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -fintrinsic-modules-path /usr/local/bin/include -g -DOFDUNAVAIL -DFFTW3UNAVAIL -DANNUNAVAIL -DMATHEVALUNAVAIL ld: warning: directory not found for option '-L/opt/local/bin/lib64' ld: warning: directory not found for option '-L/usr/local/bin/lib64' /opt/local/bin/gcc source/hdf5FCInteropC.c -o ./work/build/hdf5FCInteropC.exe -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -I/opt/local/bin/include -I/usr/local/bin/include -g -DOFDLOCKS -DOFDUNAVAIL ./work/build/hdf5FCInterop.exe > ./work/build/hdf5FCInterop.dat ./work/build/hdf5FCInteropC.exe >> ./work/build/hdf5FCInterop.dat ./scripts/build/enumerateOpenMPCriticalSections.pl pwd ./scripts/build/buildCode.pl /Users/sachi.wee/galacticus ./work/build/radiusSolverEnclosedMassTask.functionCall.xml Can't locate Sort/Topological.pm in @INC (you may need to install the Sort::Topological module) (@INC contains: /Users/sachi.wee/galacticus/perl /opt/local/lib/perl5/site_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.28 /opt/local/lib/perl5/vendor_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.28 /opt/local/lib/perl5/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/5.28) at /Users/sachi.wee/galacticus/perl/Galacticus/Build/Dependencies.pm line 9. BEGIN failed--compilation aborted at /Users/sachi.wee/galacticus/perl/Galacticus/Build/Dependencies.pm line 9. Compilation failed in require at /Users/sachi.wee/galacticus/perl/Galacticus/Build/FunctionCall.pm line 12. BEGIN failed--compilation aborted at /Users/sachi.wee/galacticus/perl/Galacticus/Build/FunctionCall.pm line 12. Compilation failed in require at ./scripts/build/buildCode.pl line 18. BEGIN failed--compilation aborted at ./scripts/build/buildCode.pl line 18. ./scripts/build/buildCode.pl /Users/sachi.wee/galacticus ./work/build/component.component.xml Can't locate Sort/Topological.pm in @INC (you may need to install the Sort::Topological module) (@INC contains: /Users/sachi.wee/galacticus/perl /opt/local/lib/perl5/site_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.28 /opt/local/lib/perl5/vendor_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.28 /opt/local/lib/perl5/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/5.28) at /Users/sachi.wee/galacticus/perl/Galacticus/Build/Dependencies.pm line 9. BEGIN failed--compilation aborted at /Users/sachi.wee/galacticus/perl/Galacticus/Build/Dependencies.pm line 9. Compilation failed in require at /Users/sachi.wee/galacticus/perl/Galacticus/Build/FunctionCall.pm line 12. BEGIN failed--compilation aborted at /Users/sachi.wee/galacticus/perl/Galacticus/Build/FunctionCall.pm line 12. Compilation failed in require at ./scripts/build/buildCode.pl line 18. BEGIN failed--compilation aborted at ./scripts/build/buildCode.pl line 18. ./scripts/build/moduleDependencies.pl pwd Can't locate Sort/Topological.pm in @INC (you may need to install the Sort::Topological module) (@INC contains: /Users/sachi.wee/galacticus/perl /opt/local/lib/perl5/site_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.28 /opt/local/lib/perl5/vendor_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.28 /opt/local/lib/perl5/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/5.28) at /Users/sachi.wee/galacticus/perl/Galacticus/Build/SourceTree/Process/FunctionClass.pm line 11. BEGIN failed--compilation aborted at /Users/sachi.wee/galacticus/perl/Galacticus/Build/SourceTree/Process/FunctionClass.pm line 11. Compilation failed in require at /Users/sachi.wee/galacticus/perl/Galacticus/Build/SourceTree.pm line 21. BEGIN failed--compilation aborted at /Users/sachi.wee/galacticus/perl/Galacticus/Build/SourceTree.pm line 21. Compilation failed in require at ./scripts/build/moduleDependencies.pl line 9. BEGIN failed--compilation aborted at ./scripts/build/moduleDependencies.pl line 9. ./scripts/build/preprocess.pl source/Galacticus.F90 ./work/build/Galacticus.p.F90 Can't locate Sort/Topological.pm in @INC (you may need to install the Sort::Topological module) (@INC contains: /Users/sachi.wee/galacticus/perl /opt/local/lib/perl5/site_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.28 /opt/local/lib/perl5/vendor_perl/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.28 /opt/local/lib/perl5/5.28/darwin-thread-multi-2level /opt/local/lib/perl5/5.28) at /Users/sachi.wee/galacticus/perl/Galacticus/Build/SourceTree/Process/FunctionClass.pm line 11. BEGIN failed--compilation aborted at /Users/sachi.wee/galacticus/perl/Galacticus/Build/SourceTree/Process/FunctionClass.pm line 11. Compilation failed in require at /Users/sachi.wee/galacticus/perl/Galacticus/Build/SourceTree.pm line 21. BEGIN failed--compilation aborted at /Users/sachi.wee/galacticus/perl/Galacticus/Build/SourceTree.pm line 21. Compilation failed in require at ./scripts/build/preprocess.pl line 6. BEGIN failed--compilation aborted at ./scripts/build/preprocess.pl line 6. make: *** [work/build/Galacticus.p.F90.up] Error 2 NABOO:galacticus sachi.wee$ which perl /opt/local/bin/perl NABOO:galacticus sachi.wee$ sudo perl -e Sort::Topological NABOO:galacticus sachi.wee$

[abensonca]

Where do you have Sort::Topological installed? You probably need to add the relevant path to the PERL5LIB variable.

[sachiwee]

I am not sure about the path. But I installed perl through MacPorts and used CPAN to install the modules

[abensonca]

Ok, so we need to know where CPAN installed the module. Did you run CPAN as sudo or as a regular user?

You could try something like

find /usr/local -name="Topological.pm"

to see if the module is installed anywhere under /use/local for example.

[sachiwee]

I ran as sudo. I get this error find: -name=Topological.pm: unknown primary or operator

[abensonca]

Ok, try

find /usr/local -name="Topological.pm"

and see if it finds Topological.pm

If not, try the same command with just /usr and with /opt

[sachiwee]

I get the same error for both

find /usr/local -name="Topological.pm" find: -name=Topological.pm: unknown primary or operator NABOO:galacticus sachi.wee$ find /opt/local -name="Topological.pm" find: -name=Topological.pm: unknown primary or operator

[abensonca]

My mistake, there should be no = after -name, just a space.

[sachiwee]

find /usr/local -name "Topological.pm" NABOO:galacticus sachi.wee$ find /opt/local -name "Topological.pm" NABOO:galacticus sachi.wee$ No output from that either

[abensonca]

Interesting!

Can you try installing Sort:: Topological again and post the output?

[sachiwee]

sudo perl -MCPAN -e 'install(Sort::Topological)' Password: Reading '/Users/sachi.wee/.cpan/Metadata' Database was generated on Fri, 10 Apr 2020 16:55:39 GMT Running install for module 'Sort::Topological' Checksum for /Users/sachi.wee/.cpan/sources/authors/id/K/KS/KSTEPHENS/Data-Match-0.06.tar.gz ok Configuring K/KS/KSTEPHENS/Data-Match-0.06.tar.gz with Makefile.PL Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Data::Match Writing MYMETA.yml and MYMETA.json KSTEPHENS/Data-Match-0.06.tar.gz /opt/local/bin/perl5.28 Makefile.PL -- OK Running make for K/KS/KSTEPHENS/Data-Match-0.06.tar.gz cp Match.pm blib/lib/Data/Match.pm cp lib/Sort/Topological.pm blib/lib/Sort/Topological.pm Manifying 2 pod documents KSTEPHENS/Data-Match-0.06.tar.gz /usr/bin/make -- OK Running make test PERL_DL_NONLAZY=1 "/opt/local/bin/perl5.28" "-Iblib/lib" "-Iblib/arch" test.pl 1..1

Running under perl version 5.028002 for darwin

Current time local: Sat Apr 11 19:22:35 2020

Current time GMT: Sun Apr 12 00:22:35 2020

Using Test.pm version 1.31

Can't use an array as a reference at blib/lib/Data/Match.pm line 968. Compilation failed in require at test.pl line 10. BEGIN failed--compilation aborted at test.pl line 10. make: *** [test_dynamic] Error 255 KSTEPHENS/Data-Match-0.06.tar.gz /usr/bin/make test -- NOT OK //hint// to see the cpan-testers results for installing this module, try: reports KSTEPHENS/Data-Match-0.06.tar.gz

[abensonca]

Ok, this is a known problem with Sort:: Topological which is causing it to fail to install. Can you try:

sudo perl -MCPAN -e 'force("install","Sort:: Topological")

and then post the output here.

[sachiwee]

Reading '/Users/sachi.wee/.cpan/Metadata' Database was generated on Fri, 10 Apr 2020 16:55:39 GMT Running install for module 'Sort::Topological' Checksum for /Users/sachi.wee/.cpan/sources/authors/id/K/KS/KSTEPHENS/Data-Match-0.06.tar.gz ok Configuring K/KS/KSTEPHENS/Data-Match-0.06.tar.gz with Makefile.PL Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Data::Match Writing MYMETA.yml and MYMETA.json KSTEPHENS/Data-Match-0.06.tar.gz /opt/local/bin/perl5.28 Makefile.PL -- OK Running make for K/KS/KSTEPHENS/Data-Match-0.06.tar.gz cp lib/Sort/Topological.pm blib/lib/Sort/Topological.pm cp Match.pm blib/lib/Data/Match.pm Manifying 2 pod documents KSTEPHENS/Data-Match-0.06.tar.gz /usr/bin/make -- OK Running make test PERL_DL_NONLAZY=1 "/opt/local/bin/perl5.28" "-Iblib/lib" "-Iblib/arch" test.pl 1..1

Running under perl version 5.028002 for darwin

Current time local: Sat Apr 11 19:49:16 2020

Current time GMT: Sun Apr 12 00:49:16 2020

Using Test.pm version 1.31

Can't use an array as a reference at blib/lib/Data/Match.pm line 968. Compilation failed in require at test.pl line 10. BEGIN failed--compilation aborted at test.pl line 10. make: *** [test_dynamic] Error 255 KSTEPHENS/Data-Match-0.06.tar.gz /usr/bin/make test -- NOT OK //hint// to see the cpan-testers results for installing this module, try: reports KSTEPHENS/Data-Match-0.06.tar.gz Running make install Manifying 2 pod documents Installing /opt/local/lib/perl5/site_perl/5.28/Sort/Topological.pm Installing /opt/local/lib/perl5/site_perl/5.28/Data/Match.pm Installing /opt/local/share/perl5.28/siteman/man3/Sort::Topological.3pm Installing /opt/local/share/perl5.28/siteman/man3/Data::Match.3pm Appending installation info to /opt/local/lib/perl5/5.28/darwin-thread-multi-2level/perllocal.pod KSTEPHENS/Data-Match-0.06.tar.gz sudo /usr/bin/make install -- OK

[abensonca]

Ok looks like it installed ok. Try compiling Galacticus again now. It will probably take at least 1 hour to build.

[sachiwee]

looks like its compiling now. Thank you so much!

[abensonca]

Great! Let me know if it succeeds.

[sachiwee]

there was another error

/opt/local/bin/gfortran -c ./work/build/structure_formation.spherical_collapse.solver.collisionlessMatter_darkEnergy.p.F90 -o ./work/build/structure_formation.spherical_collapse.solver.collisionlessMatter_darkEnergy.o -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/bin/finclude -fintrinsic-modules-path /opt/local/bin/include -fintrinsic-modules-path /opt/local/bin/include/gfortran -fintrinsic-modules-path /opt/local/bin/lib/gfortran/modules -L/opt/local/bin/lib -L/opt/local/bin/lib64 -fintrinsic-modules-path /usr/local/bin/finclude -fintrinsic-modules-path /usr/local/bin/include -fintrinsic-modules-path /usr/local/bin/include/gfortran -fintrinsic-modules-path /usr/local/bin/lib/gfortran/modules -L/usr/local/bin/lib -L/usr/local/bin/lib64 -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/lib/gfortran/modules -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran/modules -fintrinsic-modules-path /opt/local/bin/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -fintrinsic-modules-path /usr/local/bin/include -g -DOFDUNAVAIL -DFFTW3UNAVAIL -DANNUNAVAIL -DMATHEVALUNAVAIL 2>&1 | ./scripts/build/postprocess.pl ./work/build/structure_formation.spherical_collapse.solver.collisionlessMatter_darkEnergy.p.F90 /opt/local/bin/gfortran -c ./work/build/structure_formation.spherical_collapse.solver.baryons_darkMatter_darkEnergy.p.F90 -o ./work/build/structure_formation.spherical_collapse.solver.baryons_darkMatter_darkEnergy.o -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/bin/finclude -fintrinsic-modules-path /opt/local/bin/include -fintrinsic-modules-path /opt/local/bin/include/gfortran -fintrinsic-modules-path /opt/local/bin/lib/gfortran/modules -L/opt/local/bin/lib -L/opt/local/bin/lib64 -fintrinsic-modules-path /usr/local/bin/finclude -fintrinsic-modules-path /usr/local/bin/include -fintrinsic-modules-path /usr/local/bin/include/gfortran -fintrinsic-modules-path /usr/local/bin/lib/gfortran/modules -L/usr/local/bin/lib -L/usr/local/bin/lib64 -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/lib/gfortran/modules -fintrinsic-modules-path /opt/local/include/gfortran -fintrinsic-modules-path /opt/local/include -fintrinsic-modules-path /opt/local/finclude -fintrinsic-modules-path /opt/local/include/gfortran/modules -fintrinsic-modules-path /opt/local/bin/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -fintrinsic-modules-path /usr/local/bin/include -g -DOFDUNAVAIL -DFFTW3UNAVAIL -DANNUNAVAIL -DMATHEVALUNAVAIL 2>&1 | ./scripts/build/postprocess.pl ./work/build/structure_formation.spherical_collapse.solver.baryons_darkMatter_darkEnergy.p.F90 f951: internal compiler error: Segmentation fault: 11 libbacktrace could not find executable to open Please submit a full bug report, with preprocessed source if appropriate. See https://trac.macports.org/newticket for instructions. mv: rename ./work/build/moduleBuild/spherical_collapsesolvers@sphericalcollapsesolverbaryonsdarkmatterdarkenergy.smod to ./work/build/spherical_collapsesolvers@sphericalcollapsesolverbaryonsdarkmatterdarkenergy.smod: No such file or directory make: *** [work/build/structure_formation.spherical_collapse.solver.baryons_darkMatter_darkEnergy.o] Error 1

[abensonca]

Can you post the output of

gfortran -v

[sachiwee]

NABOO:galacticus sachi.wee$ gfortran -v Using built-in specs. COLLECT_GCC=gfortran COLLECT_LTO_WRAPPER=/opt/local/libexec/gcc/x86_64-apple-darwin18/10.0.1/lto-wrapper Target: x86_64-apple-darwin18 Configured with: /opt/local/var/macports/build/_opt_bblocal_var_buildworker_ports_build_ports_lang_gcc10/gcc10/work/gcc-10-20200301/configure --prefix=/opt/local --build=x86_64-apple-darwin18 --enable-languages=c,c++,objc,obj-c++,lto,fortran --libdir=/opt/local/lib/gcc10 --includedir=/opt/local/include/gcc10 --infodir=/opt/local/share/info --mandir=/opt/local/share/man --datarootdir=/opt/local/share/gcc-10 --with-local-prefix=/opt/local --with-system-zlib --disable-nls --program-suffix=-mp-10 --with-gxx-include-dir=/opt/local/include/gcc10/c++/ --with-gmp=/opt/local --with-mpfr=/opt/local --with-mpc=/opt/local --with-isl=/opt/local --enable-stage1-checking --disable-multilib --enable-lto --enable-libstdcxx-time --with-build-config=bootstrap-debug --with-as=/opt/local/bin/as --with-ld=/opt/local/bin/ld --with-ar=/opt/local/bin/ar --with-bugurl=https://trac.macports.org/newticket --disable-tls --with-pkgversion='MacPorts gcc10 10-20200301_0' --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk Thread model: posix Supported LTO compression algorithms: zlib gcc version 10.0.1 20200301 (experimental) (MacPorts gcc10 10-20200301_0)

[abensonca]

I think you'll need to try compiling a slightly older version of Galacticus that your compiler will support.

Assuming you cloned Galacticus using git you should try

git checkout 1960750cbb07ecd29e1717126b800e905233721a

and then try recompiling.

[sachiwee]

Yes I cloned Galacticus using git. Tried git checkout and waiting for it to compile now. Hopefully this works!

[sachiwee]

another error....

./scripts/build/preprocess.pl source/utility.IO.XML.F90 ./work/build/utility.IO.XML.p.F90 gfortran -c ./work/build/utility.IO.XML.p.F90 -o ./work/build/utility.IO.XML.o -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/bin/finclude -fintrinsic-modules-path /opt/local/bin/include -fintrinsic-modules-path /opt/local/bin/include/gfortran -fintrinsic-modules-path /opt/local/bin/lib/gfortran/modules -L/opt/local/bin/lib -L/opt/local/bin/lib64 -fintrinsic-modules-path /usr/local/bin/finclude -fintrinsic-modules-path /usr/local/bin/include -fintrinsic-modules-path /usr/local/bin/include/gfortran -fintrinsic-modules-path /usr/local/bin/lib/gfortran/modules -L/usr/local/bin/lib -L/usr/local/bin/lib64 -fintrinsic-modules-path /usr/local/finclude -fintrinsic-modules-path /usr/local/include/gfortran -fintrinsic-modules-path /usr/local/include -fintrinsic-modules-path /usr/lib/gfortran/modules -fintrinsic-modules-path /usr/include/gfortran -fintrinsic-modules-path /usr/include -fintrinsic-modules-path /usr/finclude -fintrinsic-modules-path /usr/lib64/gfortran/modules -fintrinsic-modules-path /usr/lib64/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -g -DOFDUNAVAIL -DFFTW3UNAVAIL -DANNUNAVAIL -DMATHEVALUNAVAIL 2>&1 | ./scripts/build/postprocess.pl ./work/build/utility.IO.XML.p.F90 source/utility.IO.XML.F90:26:9

29 | use :: FoX_dom , only : node | 1 Fatal Error: Cannot open module file 'fox_dom.mod' for reading at (1): No such file or directory compilation terminated. mv: rename ./work/build/moduleBuild/io_xml.mod to ./work/build/io_xml.mod: No such file or directory make: *** [work/build/utility.IO.XML.o] Error 1

[sachiwee]

Actually I might have a different version of FoX. Trying to install the version in the GitHub page and compile Galacticus again

[sachiwee]

Well another error

gfortran -c ./work/build/structure_formation.spherical_collapse.solver.baryons_darkMatter_darkEnergy.p.F90 -o ./work/build/structure_formation.spherical_collapse.solver.baryons_darkMatter_darkEnergy.o -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/bin/finclude -fintrinsic-modules-path /opt/local/bin/include -fintrinsic-modules-path /opt/local/bin/include/gfortran -fintrinsic-modules-path /opt/local/bin/lib/gfortran/modules -L/opt/local/bin/lib -L/opt/local/bin/lib64 -fintrinsic-modules-path /usr/local/bin/finclude -fintrinsic-modules-path /usr/local/bin/include -fintrinsic-modules-path /usr/local/bin/include/gfortran -fintrinsic-modules-path /usr/local/bin/lib/gfortran/modules -L/usr/local/bin/lib -L/usr/local/bin/lib64 -fintrinsic-modules-path /usr/local/finclude -fintrinsic-modules-path /usr/local/include/gfortran -fintrinsic-modules-path /usr/local/include -fintrinsic-modules-path /usr/lib/gfortran/modules -fintrinsic-modules-path /usr/include/gfortran -fintrinsic-modules-path /usr/include -fintrinsic-modules-path /usr/finclude -fintrinsic-modules-path /usr/lib64/gfortran/modules -fintrinsic-modules-path /usr/lib64/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -g -DOFDUNAVAIL -DFFTW3UNAVAIL -DANNUNAVAIL -DMATHEVALUNAVAIL 2>&1 | ./scripts/build/postprocess.pl ./work/build/structure_formation.spherical_collapse.solver.baryons_darkMatter_darkEnergy.p.F90 f951: internal compiler error: Segmentation fault: 11 libbacktrace could not find executable to open Please submit a full bug report, with preprocessed source if appropriate. See https://trac.macports.org/newticket for instructions. mv: rename ./work/build/moduleBuild/spherical_collapsesolvers@sphericalcollapsesolverbaryonsdarkmatterdarkenergy.smod to ./work/build/spherical_collapsesolvers@sphericalcollapsesolverbaryonsdarkmatterdarkenergy.smod: No such file or directory make: *** [work/build/structure_formation.spherical_collapse.solver.baryons_darkMatter_darkEnergy.o] Error 1

[abensonca]

It's difficult to know for to fix this as there's no useful error message given.

You could try using this revision of Galacticus and see if it works:

git checkout 304dbe0a7445f80a03d196bb685232d0b00a0057

What's happening here is that your compiler is crashing. But I can't tell why as there's no error message. So I'm trying to see if we can find an earlier version of Galacticus where it doesn't crash.

[sachiwee]

Oh ok. I will try this and see

[sachiwee]

That didn't work either

galacticus.output.version.revision.inc:3:42:

Error: Symbol 'gitbranch' at (1) already has basic type of CHARACTER source/galacticus.output.version.F90:87:51

114 | call versionGroup%writeAttribute(trim(buildTime),'buildTime') | 1 Error: Symbol 'buildtime' at (1) has no IMPLICIT type; did you mean 'runtime'? source/galacticus.output.version.F90:53:124

73 | Galacticus_Version_String=var_str("revision ")//gitHash//" (branch: "//trim(gitBranch)//"; build time: "//trim(buildTime)//")" | 1 Error: Symbol 'buildtime' at (1) has no IMPLICIT type source/galacticus.output.version.F90:42:56

56 | if (present(buildTime )) buildTime =trim(buildTime) | 1 Error: Symbol 'buildtime' at (1) has no IMPLICIT type; did you mean 'buildtime_'? source/galacticus.output.version.F90:87:21

114 | call versionGroup%writeAttribute(trim(buildTime),'buildTime') | 1 Error: Found no matching specific binding for the call to the GENERIC 'writeattribute' at (1) make: *** [work/build/galacticus.output.version.o] Error 1 rm work/build/objects.nodes.components.basic.non_evolving.bound_functions.Inc work/build/objects.nodes.components.basic.standard.bound_functions.Inc

[abensonca]

Ok. Unfortunately I'm out of ideas. You could try other revisions of Galacticus and see if you can find a version that works.

If I can find time I'll see if I can install a Mac OS virtual machine and try installing it myself in there.

[sachiwee]

Ok. I will keep trying. Thank you very much for your help!

[Xiaolong-Du]

@sachiwee The error

Error: Symbol 'gitbranch' at (1) already has basic type of CHARACTER

seems to be a known issue with the Makefile, which has been resolved in the latest version. The problem is caused by an inappropriate treatment of the branch name when it starts with "*". Try to replace the following line in the Makefile

@if [ -f .git/refs/heads/master ] ; then git branch | awk '{print "character(len=128), parameter :: gitBranch=\""$$2"\""}' >> $(BUILDPATH)/galacticus.output.version.revision.inc; else printf 'character(len=128), parameter :: gitBranch="(unknown)"\n' >> $(BUILDPATH)/galacticus.output.version.revision.inc; fi

with

@if [ -f .git/refs/heads/master ] ; then git branch | awk '{if ($$1 == "*") print "character(len=128), parameter :: gitBranch=\""$$2"\""}' >> $(BUILDPATH)/galacticus.output.version.revision.inc; else printf 'character(len=128), parameter :: gitBranch="(unknown)"\n' >> $(BUILDPATH)/galacticus.output.version.revision.inc; fi

Then delete the build folder "./work" and recompile Galacticus. If it still does not compile successfully, I can try to install Galacticus on my mac and try if I can figure out what went wrong.

[sachiwee]

@Xiaolong-Du I tried that but now I get another error

gfortran -c source/fftw3_config.F90 -o ./work/build/fftw3_config.o -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/bin/finclude -fintrinsic-modules-path /opt/local/bin/include -fintrinsic-modules-path /opt/local/bin/include/gfortran -fintrinsic-modules-path /opt/local/bin/lib/gfortran/modules -L/opt/local/bin/lib -L/opt/local/bin/lib64 -fintrinsic-modules-path /usr/local/bin/finclude -fintrinsic-modules-path /usr/local/bin/include -fintrinsic-modules-path /usr/local/bin/include/gfortran -fintrinsic-modules-path /usr/local/bin/lib/gfortran/modules -L/usr/local/bin/lib -L/usr/local/bin/lib64 -fintrinsic-modules-path /usr/local/finclude -fintrinsic-modules-path /usr/local/include/gfortran -fintrinsic-modules-path /usr/local/include -fintrinsic-modules-path /usr/lib/gfortran/modules -fintrinsic-modules-path /usr/include/gfortran -fintrinsic-modules-path /usr/include -fintrinsic-modules-path /usr/finclude -fintrinsic-modules-path /usr/lib64/gfortran/modules -fintrinsic-modules-path /usr/lib64/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -g > /dev/null 2>&1 ; \ if [ $? -eq 0 ] ; then \ echo "FCFLAGS += -DFFTW3AVAIL" > ./work/build/Makefile_Config_FFTW3 ; \ else \ echo "FCFLAGS += -DFFTW3UNAVAIL" > ./work/build/Makefile_Config_FFTW3 ; \ fi gfortran source/hdf5FCInterop.F90 -o ./work/build/hdf5FCInterop.exe -ffree-line-length-none -frecursive -DBUILDPATH=\'./work/build\' -J./work/build/moduleBuild/ -I./work/build/ -fintrinsic-modules-path /opt/local/bin/finclude -fintrinsic-modules-path /opt/local/bin/include -fintrinsic-modules-path /opt/local/bin/include/gfortran -fintrinsic-modules-path /opt/local/bin/lib/gfortran/modules -L/opt/local/bin/lib -L/opt/local/bin/lib64 -fintrinsic-modules-path /usr/local/bin/finclude -fintrinsic-modules-path /usr/local/bin/include -fintrinsic-modules-path /usr/local/bin/include/gfortran -fintrinsic-modules-path /usr/local/bin/lib/gfortran/modules -L/usr/local/bin/lib -L/usr/local/bin/lib64 -fintrinsic-modules-path /usr/local/finclude -fintrinsic-modules-path /usr/local/include/gfortran -fintrinsic-modules-path /usr/local/include -fintrinsic-modules-path /usr/lib/gfortran/modules -fintrinsic-modules-path /usr/include/gfortran -fintrinsic-modules-path /usr/include -fintrinsic-modules-path /usr/finclude -fintrinsic-modules-path /usr/lib64/gfortran/modules -fintrinsic-modules-path /usr/lib64/openmpi/lib -pthread -Wall -fbacktrace -ffpe-trap=invalid,zero,overflow -fdump-core -O3 -ffinite-math-only -fno-math-errno -fopenmp -g -DFFTW3UNAVAIL -DANNUNAVAIL -DMATHEVALUNAVAIL make: gfortran: No such file or directory

[abensonca]

That's strange - it's been able to find gfortran before.

What does

which gfortran

show?

[sachiwee]

it doesn't return anything

[abensonca]

Very strange. It seems to have lost where you installed gfortran. Maybe you need to reset your PATH variable to include the path to where you installed gfortran.

[Xiaolong-Du]

I aggreed with Andrew. You can try adding the directory where you install gcc to PATH.

PS. When you replace the line in the Makeifile as mentioned above, be careful that there might be preoblems with copying and pasting for some special characters. So instread of copy the whole line, just make the changes directly in the original file. Basically, the fix only add

if ($$1 == "*")

before

... print "character(len=128), parameter :: gitBranch=\""$$2"\""}' ...

[sachiwee]

there is another version of gcc in /usr/bin and seems to be in the path instead of the version in /opt/local/bin/gcc

[abensonca]

Try

export PATH=/opt/local/bin:$PATH

and see if it can then find gfortran when you do

which gfortran