Closed liempi closed 2 years ago
abensonca
commented
2 years ago Can you try removing the build directory and then making again sending the output to a log file? Like this:
rm -rf work/build
make Galacticus.exe >& make.logand then post the make.log here?
liempi
commented
2 years ago Here is the make.log file:
./scripts/build/findExecutables.pl pwd
./scripts/build/codeDirectivesParse.pl pwd
./scripts/build/stateStorables.pl pwd
./scripts/build/deepCopyActions.pl pwd
./scripts/build/includeDependencies.pl pwd
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
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
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 /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
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
gcc source/proc_config.c -o ./work/build/proc_config -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -g -DOFDLOCKS > /dev/null 2>&1 ; \
if [ $? -eq 0 ] ; then \
./work/build/proc_config > /dev/null 2>&1 ; \
if [ $? -eq 0 ] ; then \
echo "FCFLAGS += -DPROCPS" > ./work/build/Makefile_Config_Proc ; \
echo "CFLAGS += -DPROCPS" >> ./work/build/Makefile_Config_Proc ; \
echo "CPPFLAGS += -DPROCPS" >> ./work/build/Makefile_Config_Proc ; \
fi \
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 /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
gcc source/hdf5FCInteropC.c -o ./work/build/hdf5FCInteropC.exe -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -g -DOFDLOCKS -DOFDUNAVAIL
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
./scripts/build/moduleDependencies.pl pwd
gcc source/hdf5FCInteropC.c -o ./work/build/hdf5FCInteropC.exe -DBUILDPATH=\'./work/build\' -I./source/ -I./work/build/ -fopenmp -g -DOFDLOCKS -DOFDUNAVAIL
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
abensonca
commented
2 years ago It looks like it's trying to run clang, so I assume you're trying to build Galacticus on a Mac? If so, we've only just recently gotten this to work, so there may still be some issues to work out. Are you following the instructions at https://github.com/galacticusorg/galacticus/wiki/Installation-from-source-on-MacOS ?
liempi
commented
2 years ago I didn't see this, I'll try again! thanks.
abensonca
commented
2 years ago Sounds good! Let me know if you run into problems, or if it's successful.
abensonca
commented
2 years ago Also, there's an experimental precompiled executable for MacOS that may be useful: https://github.com/galacticusorg/galacticus/wiki/Using-Precompiled-Binaries-on-MacOS
liempi
commented
2 years ago Tutorial didn't work and the precompiled said that Galacticus.exe is a Microsoft executable. I don't know what is wrong
abensonca
commented
2 years ago Can you provide details of what didn't work when you tried to build? And what's the full error message you get when trying to run the pre-compiled binary?
Xiaolong-Du
commented
2 years ago @liempi I just did some tests on the pre-compiled binary for MacOS. The test runs fine. If you follow step 1 and step 2 as shown in the Tutorial Andrew mentioned above. You should get all the necessary files. I am not sure why the command "Curl" does not work for me. But anyway, you need to download the "Galacticus" repository and "datasets" repository to run the quick test in step 2.
The zip file containing precompiled executable does not include the static dataset, so you will need to copy the "datasets/static" folder from step 1 to "datasets" you get from the zip file.
The parameter file for the quick test, "quickTest.xml", is included in the source file of Galacticus from step 1, so you need to copy the "parameters" folder from step 1 to where you have the file Galacticus.exe.
If you have all the files mentioned above, you can run the quick test as shown in Tutorial:
./Galacticus.exe parameters/quickTest.xml
When you run this for the first time, you will get a message that "Galacticus.exe can not be opened because the developer cannot be verified". Just click "cancel". Go to "System Preferences"->"Security & Privacy" ->"General", where you will see "Galacticus.exe was blocked ...". Click "Allow anyway". Then try to rerun Galactiuus. You may again get similar error message, but for another executable file. Repeat the above steps to allow the executable to run. After a few attempts, you should be able to run the test. Note that if you get error message related to "datasets", try removing all the files under "datasets/dynamic/intergalacticMedium" and "datasets/dynamic/largeScaleStructure".
I hope this can solve the problem you met.
abensonca
commented
2 years ago Thanks @Xiaolong-Du - I will update the installation notes to include these points.
liempi
commented
2 years ago Sorry for the delay, I found my error. When I try to install hdf5 the log file returns: ./configure: line 3453: gcc-11.2: command not found
so, I think the problem is with the gcc installation but the installation of gcc is ok.
liempi
commented
2 years ago @liempi I just did some tests on the pre-compiled binary for MacOS. The test runs fine. If you follow step 1 and step 2 as shown in the Tutorial Andrew mentioned above. You should get all the necessary files. I am not sure why the command "Curl" does not work for me. But anyway, you need to download the "Galacticus" repository and "datasets" repository to run the quick test in step 2.
The zip file containing precompiled executable does not include the static dataset, so you will need to copy the "datasets/static" folder from step 1 to "datasets" you get from the zip file.
The parameter file for the quick test, "quickTest.xml", is included in the source file of Galacticus from step 1, so you need to copy the "parameters" folder from step 1 to where you have the file Galacticus.exe.
If you have all the files mentioned above, you can run the quick test as shown in Tutorial:
./Galacticus.exe parameters/quickTest.xml
When you run this for the first time, you will get a message that "Galacticus.exe can not be opened because the developer cannot be verified". Just click "cancel". Go to "System Preferences"->"Security & Privacy" ->"General", where you will see "Galacticus.exe was blocked ...". Click "Allow anyway". Then try to rerun Galactiuus. You may again get similar error message, but for another executable file. Repeat the above steps to allow the executable to run. After a few attempts, you should be able to run the test. Note that if you get error message related to "datasets", try removing all the files under "datasets/dynamic/intergalacticMedium" and "datasets/dynamic/largeScaleStructure".
I hope this can solve the problem you met.
liempi@MacBook-Pro-de-Matias galacticus % sudo ./Galacticus.exe parameters/quickTest.xml
## © 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021
M: Memory: nodes + misc = total M: 1.000 b + 9.000 b = 10.000 b M: Memory: nodes + misc = total M: 1.000 b + 17.000 b = 18.000 b M: Memory: nodes + misc = total M: 1.000 b + 25.000 b = 26.000 b M: Memory: nodes + misc = total M: 1.000 b + 33.000 b = 34.000 b M: Memory: nodes + misc = total M: 1.000 b + 49.000 b = 50.000 b M: Memory: nodes + misc = total M: 1.000 b + 13.196kib = 13.197kib M: Memory: nodes + misc = total M: 1.000 b + 26.345kib = 26.346kib M: Memory: nodes + misc = total M: 1.000 b + 40.228kib = 40.229kib M: Memory: nodes + misc = total M: 1.000 b + 54.095kib = 54.096kib M: Memory: nodes + misc = total M: 1.000 b + 44.540kib = 44.541kib M: Memory: nodes + misc = total M: 1.000 b + 59.845kib = 59.846kib M: Memory: nodes + misc = total M: 1.000 b + 48.853kib = 48.854kib M: Memory: nodes + misc = total M: 1.000 b + 65.595kib = 65.596kib M: Memory: nodes + misc = total M: 1.000 b + 53.165kib = 53.166kib M: Memory: nodes + misc = total M: 1.000 b + 71.345kib = 71.346kib Fatal error: Unable to find data file "./static/darkMatter/Halo_Mass_Function_Parameters_Tinker_2008.xml" Occurred at: function:tinker2008ConstructorInternal file:structure_formation.halo_mass_function.Tinker2008.F90 [line 158] => Error occurred in master thread
Program aborted. Backtrace:
I tried and I got this in my shell, but I check the directory and the file is exactly there.
abensonca
commented
2 years ago For the pre-compiled case the problem is that Galacticus is unable to find the datasets that it needs at run time.
Did you download and unpack the datasets? This is described in this step of the instructions:
mkdir ~/Galacticus
cd ~/Galacticus
curl https://github.com/galacticusorg/galacticus/archive/master.zip --output galacticus.zip
curl https://github.com/galacticusorg/datasets/archive/master.zip --output datasets.zip
unzip galacticus.zip
unzip datasets.zipDid you set environment variables to point to where they are installed? For example if you followed the instructions in the tutorial the datasets world be in ~/Galacticus/datasets so you would need to set:
export GALACTICUS_DATA_PATH=~/Galacticus/datasetsSorry for the delay, I found my error. When I try to install hdf5 the log file returns: ./configure: line 3453: gcc-11.2: command not found
so, I think the problem is with the gcc installation but the installation of gcc is ok.
It's possible that you need to set your PATH variable to include the location where gcc-11.2 was installed.
First, check whether you have gcc-11.2 in /usr/local/gcc-11.2.0/bin. If so, you can do:
export PATH=/usr/local/gcc-11.2.0/bin:$PATHto add this location to your PATH.
I see that there's an error in the instructions for this step on the wiki page, I'll fix that now.
liempi
commented
2 years ago @abensonca Now is working, I'm gonna reinstall from the source, maybe now it will work. Thanks for your time!!
Hello, I'm trying to install Galacticus but when I type make in my shell I obtain:
File does not exist: ./work/build/stateStorables.xml at /usr/local/Cellar/perl/5.34.0/lib/perl5/site_perl/5.34.0/XML/Simple.pm line 981. XML::Simple::find_xml_file(XML::Simple=HASH(0x7fb4cf8f4cd0), "./work/build/stateStorables.xml") called at /usr/local/Cellar/perl/5.34.0/lib/perl5/site_perl/5.34.0/XML/Simple.pm line 238 XML::Simple::parse_file(XML::Simple=HASH(0x7fb4cf8f4cd0), "./work/build/stateStorables.xml") called at /usr/local/Cellar/perl/5.34.0/lib/perl5/site_perl/5.34.0/XML/Simple.pm line 218 XML::Simple::XMLin(XML::Simple=HASH(0x7fb4cf8f4cd0), "./work/build/stateStorables.xml") called at /Users/liempi/Documents/galacticus/perl/Galacticus/Build/SourceTree/Process/ObjectBuilder.pm line 51 Galacticus::Build::SourceTree::Process::ObjectBuilder::Process_ObjectBuilder(HASH(0x7fb4c8c15e88), HASH(0x7fb4c89e5380)) called at /Users/liempi/Documents/galacticus/perl/Galacticus/Build/SourceTree.pm line 184 Galacticus::Build::SourceTree::ProcessTree(HASH(0x7fb4c8c15e88)) called at ./scripts/build/buildCode.pl line 217 at /Users/liempi/Documents/galacticus/perl/Galacticus/Build/Components.pm line 69. Galacticus::Build::Components::ANON("File does not exist: ./work/build/stateStorables.xml at /usr/"...) called at /usr/local/Cellar/perl/5.34.0/lib/perl5/5.34.0/Carp.pm line 291 Carp::croak("File does not exist: ./work/build/stateStorables.xml") called at /usr/local/Cellar/perl/5.34.0/lib/perl5/site_perl/5.34.0/XML/Simple.pm line 981 XML::Simple::find_xml_file(XML::Simple=HASH(0x7fb4cf8f4cd0), "./work/build/stateStorables.xml") called at /usr/local/Cellar/perl/5.34.0/lib/perl5/site_perl/5.34.0/XML/Simple.pm line 238 XML::Simple::parse_file(XML::Simple=HASH(0x7fb4cf8f4cd0), "./work/build/stateStorables.xml") called at /usr/local/Cellar/perl/5.34.0/lib/perl5/site_perl/5.34.0/XML/Simple.pm line 218 XML::Simple::XMLin(XML::Simple=HASH(0x7fb4cf8f4cd0), "./work/build/stateStorables.xml") called at /Users/liempi/Documents/galacticus/perl/Galacticus/Build/SourceTree/Process/ObjectBuilder.pm line 51 Galacticus::Build::SourceTree::Process::ObjectBuilder::Process_ObjectBuilder(HASH(0x7fb4c8c15e88), HASH(0x7fb4c89e5380)) called at /Users/liempi/Documents/galacticus/perl/Galacticus/Build/SourceTree.pm line 184 Galacticus::Build::SourceTree::ProcessTree(HASH(0x7fb4c8c15e88)) called at ./scripts/build/buildCode.pl line 217