Issue When I run Make #198

liempi · 2021-10-09T00:29:47Z

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

abensonca · 2021-10-09T00:34:41Z

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.log

and then post the make.log here?

liempi · 2021-10-09T00:39:05Z

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 · 2021-10-09T00:43:34Z

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 · 2021-10-09T00:46:45Z

I didn't see this, I'll try again! thanks.

abensonca · 2021-10-09T00:47:42Z

Sounds good! Let me know if you run into problems, or if it's successful.

abensonca · 2021-10-09T00:59:02Z

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 · 2021-10-09T04:10:09Z

Tutorial didn't work and the precompiled said that Galacticus.exe is a Microsoft executable. I don't know what is wrong

abensonca · 2021-10-09T04:12:46Z

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 · 2021-10-09T05:41:24Z

@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 · 2021-10-09T05:45:53Z

Thanks @Xiaolong-Du - I will update the installation notes to include these points.

liempi · 2021-10-09T12:54:11Z

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 · 2021-10-09T13:16:04Z

@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

##

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### ### # ### # # # # # #

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#### ### #### ### ## ### ### ####

© 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016,
2017, 2018, 2019, 2020, 2021

Andrew Benson

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
#0 0x10f00bbee
#1 0x10d81c6d4
#2 0x10d81c845
#3 0x10e74f984
#4 0x10e750a87
#5 0x10e776360
#6 0x10e77a374
#7 0x10dd06535
#8 0x10dd31b62
#9 0x10dd35084
#10 0x10e847894
#11 0x10e8d8975
#12 0x10e8e13d4
#13 0x10d50d5ad
#14 0x10f05c808

Program aborted. Backtrace:
#0 0x10f00bbee
#1 0x10f00c757
#2 0x10f04a6f8
#3 0x10d81c727
#4 0x10d81c845
#5 0x10e74f984
#6 0x10e750a87
#7 0x10e776360
#8 0x10e77a374
#9 0x10dd06535
#10 0x10dd31b62
#11 0x10dd35084
#12 0x10e847894
#13 0x10e8d8975
#14 0x10e8e13d4
#15 0x10d50d5ad
#16 0x10f05c808

I tried and I got this in my shell, but I check the directory and the file is exactly there.

abensonca · 2021-10-09T13:47:04Z

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.zip

Did 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/datasets

abensonca · 2021-10-09T13:52:05Z

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.

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:$PATH

to 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 · 2021-10-09T14:03:27Z

@abensonca Now is working, I'm gonna reinstall from the source, maybe now it will work. Thanks for your time!!

liempi changed the title ~~Issue When I ran Make~~ Issue When I run Make Oct 9, 2021

liempi closed this as completed Feb 6, 2022

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Issue When I run Make #198

Issue When I run Make #198

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Issue When I run Make #198

Issue When I run Make #198

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