Hi,
I hope someone can help. I have tried to install the Einstein Toolkit but am getting an error in the final part of the process on the Jupyter CactusTutorial:
%%bash ./simfactory/bin/sim build -j2 --thornlist thornlists/einsteintoolkit.th
Output is:
Using configuration: sim Reconfiguring sim Writing configuration to: /Users/rob/Cactus/configs/sim/OptionList Cactus - version: 4.14.0 Reconfiguring sim. Using configuration options from configure line Setting fds to '3,5 -j --' End of options from configure line Adding configuration options from '/Users/rob/Cactus/configs/sim/OptionList'... Setting VERSION to '2018-12-13' Setting CPP to 'cpp' Setting CC to 'gcc' Setting CXX to 'g++' Setting FPP to 'cpp' Setting F90 to 'gfortran' Setting CPPFLAGS to '' Setting FPPFLAGS to '-traditional' Setting CFLAGS to '-g -std=gnu99' Setting CXXFLAGS to '-g -std=gnu++11' Setting F90FLAGS to '-g -fcray-pointer -ffixed-line-length-none' Setting LDFLAGS to '-rdynamic' Setting DEBUG to 'no' Setting CPP_DEBUG_FLAGS to '' Setting C_DEBUG_FLAGS to '' Setting CXX_DEBUG_FLAGS to '' Setting OPTIMISE to 'yes' Setting CPP_OPTIMISE_FLAGS to '' Setting C_OPTIMISE_FLAGS to '-O2' Setting CXX_OPTIMISE_FLAGS to '-O2' Setting F90_OPTIMISE_FLAGS to '-O2' Setting PROFILE to 'no' Setting CPP_PROFILE_FLAGS to '' Setting C_PROFILE_FLAGS to '-pg' Setting CXX_PROFILE_FLAGS to '-pg' Setting F90_PROFILE_FLAGS to '-pg' Setting WARN to 'yes' Setting CPP_WARN_FLAGS to '-Wall' Setting C_WARN_FLAGS to '-Wall' Setting CXX_WARN_FLAGS to '-Wall' Setting F90_WARN_FLAGS to '-Wall' Setting OPENMP to 'yes' Setting CPP_OPENMP_FLAGS to '-fopenmp' Setting FPP_OPENMP_FLAGS to '-D_OPENMP' Setting C_OPENMP_FLAGS to '-fopenmp' Setting CXX_OPENMP_FLAGS to '-fopenmp' Setting F90_OPENMP_FLAGS to '-fopenmp' Setting VECTORISE to 'yes' Setting VECTORISE_ALIGNED_ARRAYS to 'no' Setting VECTORISE_INLINE to 'yes' Setting PTHREADS_DIR to 'NO_BUILD' End of options from '/Users/rob/Cactus/configs/sim/OptionList'. creating cache ./config.cache checking host system type... x86_64-apple-darwin22.5.0 checking for mawk... no checking for gawk... no checking for nawk... no checking for awk... awk checking whether make sets ${MAKE}... yes checking whether the C compiler (gcc -g -std=gnu99 -rdynamic) works... yes checking whether the C compiler (gcc -g -std=gnu99 -rdynamic) is a cross-compiler... no checking whether we are using GNU C... yes checking whether the C++ compiler (g++ -g -std=gnu++11 -rdynamic) works... yes checking whether the C++ compiler (g++ -g -std=gnu++11 -rdynamic) is a cross-compiler... no checking whether we are using GNU C++... yes checking for nvcc... no checking for ranlib... ranlib checking for perl... perl checking for gtar... no checking for tar... tar checking for xargs... xargs checking for gzip... gzip checking for gpatch... no checking for patch... patch checking for git... git checking for ar... ar checking for mkdir... mkdir checking for bash... /bin/sh Unknown MacOS X f90 compiler. Please add appropriate information to /Users/rob/Cactus/lib/make/known-architectures/darwin and send the updated file to CactusMaint We will try anyway ... checking whether the Fortran compiler (gfortran ) works... no configure: error: installation or configuration problem: Fortran compiler cannot create executables (see configs/sim/config-data/config.log for details).
Error reconfiguring sim-config make: *** [sim-config] Error 2
As you can see I get an error where it does not like the fortran compiler.
I have tried all of the precursor stuff a number of times using both MacPorts and Homebrew and this does not seem to give any errors when installing.
I seem to be going round in circles to resolve this, if you are able to help that would be really appreciated.
Rob
Hello Bob,
You said you followed the jupyter tutorial and the log output would seem to indicate that you did, but just to be sure: did you make sure to install the prerequisites listed on
https://github.com/einsteintoolkit/jupyter-et/blob/master/tutorial-server/no...
ie for a Mac:
--8<-- On Mac, please first
Install Xcode from the Apple App Store. In addition agree to Xcode license and install the Xcode Command Line Tools in Terminal
sudo xcodebuild -license sudo xcode-select --install
when using MacPorts install MacPorts for your version of the Mac operating system, if you have not already installed it (https://www.macports.org/install.php). Next, please install the following packages, using the commands:
sudo port -N install pkgconfig gcc12 openmpi-gcc12 fftw-3 gsl zlib openssl subversion ld64 hdf5 +fortran +gfortran sudo port select mpi openmpi-gcc12-fortran sudo port select gcc mp-gcc12
when using HomeBrew install HomeBrew for your version of the Mac operating system, if you have not already installed it (https://brew.sh/). make sure to add /opt/homebrew/bin to your PATH as instructed by the installation script. You may need to restart your terminal. Next, please install the following packages, using the commands:
brew install fftw gcc gsl hdf5 hwloc jpeg open-mpi openssl zlib pkg-config bash subversion brew link --force jpeg openssl zlib
--8<--
Also could you attach the config.log file that the error message refers to, please? This is file configs/sim/config-data/config.log ? It will contain the exact error message that the attempt to use gfortran as the Fortran compiler produced.
Yours, Roland
Hi,
I hope someone can help. I have tried to install the Einstein Toolkit but am getting an error in the final part of the process on the Jupyter CactusTutorial:
%%bash ./simfactory/bin/sim build -j2 --thornlist thornlists/einsteintoolkit.th
Output is:
Using configuration: sim Reconfiguring sim Writing configuration to: /Users/rob/Cactus/configs/sim/OptionList Cactus - version: 4.14.0 Reconfiguring sim. Using configuration options from configure line Setting fds to '3,5 -j --' End of options from configure line Adding configuration options from '/Users/rob/Cactus/configs/sim/OptionList'... Setting VERSION to '2018-12-13' Setting CPP to 'cpp' Setting CC to 'gcc' Setting CXX to 'g++' Setting FPP to 'cpp' Setting F90 to 'gfortran' Setting CPPFLAGS to '' Setting FPPFLAGS to '-traditional' Setting CFLAGS to '-g -std=gnu99' Setting CXXFLAGS to '-g -std=gnu++11' Setting F90FLAGS to '-g -fcray-pointer -ffixed-line-length-none' Setting LDFLAGS to '-rdynamic' Setting DEBUG to 'no' Setting CPP_DEBUG_FLAGS to '' Setting C_DEBUG_FLAGS to '' Setting CXX_DEBUG_FLAGS to '' Setting OPTIMISE to 'yes' Setting CPP_OPTIMISE_FLAGS to '' Setting C_OPTIMISE_FLAGS to '-O2' Setting CXX_OPTIMISE_FLAGS to '-O2' Setting F90_OPTIMISE_FLAGS to '-O2' Setting PROFILE to 'no' Setting CPP_PROFILE_FLAGS to '' Setting C_PROFILE_FLAGS to '-pg' Setting CXX_PROFILE_FLAGS to '-pg' Setting F90_PROFILE_FLAGS to '-pg' Setting WARN to 'yes' Setting CPP_WARN_FLAGS to '-Wall' Setting C_WARN_FLAGS to '-Wall' Setting CXX_WARN_FLAGS to '-Wall' Setting F90_WARN_FLAGS to '-Wall' Setting OPENMP to 'yes' Setting CPP_OPENMP_FLAGS to '-fopenmp' Setting FPP_OPENMP_FLAGS to '-D_OPENMP' Setting C_OPENMP_FLAGS to '-fopenmp' Setting CXX_OPENMP_FLAGS to '-fopenmp' Setting F90_OPENMP_FLAGS to '-fopenmp' Setting VECTORISE to 'yes' Setting VECTORISE_ALIGNED_ARRAYS to 'no' Setting VECTORISE_INLINE to 'yes' Setting PTHREADS_DIR to 'NO_BUILD' End of options from '/Users/rob/Cactus/configs/sim/OptionList'. creating cache ./config.cache checking host system type... x86_64-apple-darwin22.5.0 checking for mawk... no checking for gawk... no checking for nawk... no checking for awk... awk checking whether make sets ${MAKE}... yes checking whether the C compiler (gcc -g -std=gnu99 -rdynamic) works... yes checking whether the C compiler (gcc -g -std=gnu99 -rdynamic) is a cross-compiler... no checking whether we are using GNU C... yes checking whether the C++ compiler (g++ -g -std=gnu++11 -rdynamic) works... yes checking whether the C++ compiler (g++ -g -std=gnu++11 -rdynamic) is a cross-compiler... no checking whether we are using GNU C++... yes checking for nvcc... no checking for ranlib... ranlib checking for perl... perl checking for gtar... no checking for tar... tar checking for xargs... xargs checking for gzip... gzip checking for gpatch... no checking for patch... patch checking for git... git checking for ar... ar checking for mkdir... mkdir checking for bash... /bin/sh Unknown MacOS X f90 compiler. Please add appropriate information to /Users/rob/Cactus/lib/make/known-architectures/darwin and send the updated file to CactusMaint We will try anyway ... checking whether the Fortran compiler (gfortran ) works... no configure: error: installation or configuration problem: Fortran compiler cannot create executables (see configs/sim/config-data/config.log for details).
Error reconfiguring sim-config make: *** [sim-config] Error 2
As you can see I get an error where it does not like the fortran compiler.
I have tried all of the precursor stuff a number of times using both MacPorts and Homebrew and this does not seem to give any errors when installing.
I seem to be going round in circles to resolve this, if you are able to help that would be really appreciated.
Rob
Yours, Roland
Thank you Roland for your reply, I was just watching your Youtube video "Introduction to the Einstein Toolkit", so seeing your name pop up was a bit of a surprise!!
I believe that I had previously done everything required and followed all of the install instructions properly. But I have now gone through them all again and still have the same problem. I have attached the config file you mentioned but it doesn't seem to give any more details that are spooled in the Jupyter notebook when I run it.
Regards
Rob
On Mon, 7 Aug 2023 at 14:50, Roland Haas rhaas@illinois.edu wrote:
Hello Bob,
You said you followed the jupyter tutorial and the log output would seem to indicate that you did, but just to be sure: did you make sure to install the prerequisites listed on
https://github.com/einsteintoolkit/jupyter-et/blob/master/tutorial-server/no...
ie for a Mac:
--8<-- On Mac, please first
Install Xcode from the Apple App Store. In addition agree to Xcodelicense and install the Xcode Command Line Tools in Terminal
sudo xcodebuild -license sudo xcode-select --install
when using MacPorts install MacPorts for your version of the Mac operating system, ifyou have not already installed it (https://www.macports.org/install.php). Next, please install the following packages, using the commands:
sudo port -N install pkgconfig gcc12 openmpi-gcc12 fftw-3 gsl zlib openssl subversion ld64 hdf5 +fortran +gfortran sudo port select mpi openmpi-gcc12-fortran sudo port select gcc mp-gcc12
when using HomeBrew install HomeBrew for your version of the Mac operating system, ifyou have not already installed it (https://brew.sh/). make sure to add /opt/homebrew/bin to your PATH as instructed by the installation script. You may need to restart your terminal. Next, please install the following packages, using the commands:
brew install fftw gcc gsl hdf5 hwloc jpeg open-mpi openssl zlib pkg-config bash subversion brew link --force jpeg openssl zlib
--8<--
Also could you attach the config.log file that the error message refers to, please? This is file configs/sim/config-data/config.log ? It will contain the exact error message that the attempt to use gfortran as the Fortran compiler produced.
Yours, Roland
Hi,
I hope someone can help. I have tried to install the Einstein Toolkit but am getting an error in
the
final part of the process on the Jupyter CactusTutorial:
%%bash ./simfactory/bin/sim build -j2 --thornlist thornlists/einsteintoolkit.th
Output is:
Using configuration: sim Reconfiguring sim Writing configuration to: /Users/rob/Cactus/configs/sim/OptionList Cactus - version: 4.14.0 Reconfiguring sim. Using configuration options from configure line Setting fds to '3,5 -j --' End of options from configure line Adding configuration options from
'/Users/rob/Cactus/configs/sim/OptionList'...
Setting VERSION to '2018-12-13' Setting CPP to 'cpp' Setting CC to 'gcc' Setting CXX to 'g++' Setting FPP to 'cpp' Setting F90 to 'gfortran' Setting CPPFLAGS to '' Setting FPPFLAGS to '-traditional' Setting CFLAGS to '-g -std=gnu99' Setting CXXFLAGS to '-g -std=gnu++11' Setting F90FLAGS to '-g -fcray-pointer -ffixed-line-length-none' Setting LDFLAGS to '-rdynamic' Setting DEBUG to 'no' Setting CPP_DEBUG_FLAGS to '' Setting C_DEBUG_FLAGS to '' Setting CXX_DEBUG_FLAGS to '' Setting OPTIMISE to 'yes' Setting CPP_OPTIMISE_FLAGS to '' Setting C_OPTIMISE_FLAGS to '-O2' Setting CXX_OPTIMISE_FLAGS to '-O2' Setting F90_OPTIMISE_FLAGS to '-O2' Setting PROFILE to 'no' Setting CPP_PROFILE_FLAGS to '' Setting C_PROFILE_FLAGS to '-pg' Setting CXX_PROFILE_FLAGS to '-pg' Setting F90_PROFILE_FLAGS to '-pg' Setting WARN to 'yes' Setting CPP_WARN_FLAGS to '-Wall' Setting C_WARN_FLAGS to '-Wall' Setting CXX_WARN_FLAGS to '-Wall' Setting F90_WARN_FLAGS to '-Wall' Setting OPENMP to 'yes' Setting CPP_OPENMP_FLAGS to '-fopenmp' Setting FPP_OPENMP_FLAGS to '-D_OPENMP' Setting C_OPENMP_FLAGS to '-fopenmp' Setting CXX_OPENMP_FLAGS to '-fopenmp' Setting F90_OPENMP_FLAGS to '-fopenmp' Setting VECTORISE to 'yes' Setting VECTORISE_ALIGNED_ARRAYS to 'no' Setting VECTORISE_INLINE to 'yes' Setting PTHREADS_DIR to 'NO_BUILD' End of options from '/Users/rob/Cactus/configs/sim/OptionList'. creating cache ./config.cache checking host system type... x86_64-apple-darwin22.5.0 checking for mawk... no checking for gawk... no checking for nawk... no checking for awk... awk checking whether make sets ${MAKE}... yes checking whether the C compiler (gcc -g -std=gnu99 -rdynamic) works...
yes
checking whether the C compiler (gcc -g -std=gnu99 -rdynamic) is a cross-compiler... no checking whether we are using GNU C... yes checking whether the C++ compiler (g++ -g -std=gnu++11 -rdynamic)
works... yes
checking whether the C++ compiler (g++ -g -std=gnu++11 -rdynamic) is a cross-compiler... no checking whether we are using GNU C++... yes checking for nvcc... no checking for ranlib... ranlib checking for perl... perl checking for gtar... no checking for tar... tar checking for xargs... xargs checking for gzip... gzip checking for gpatch... no checking for patch... patch checking for git... git checking for ar... ar checking for mkdir... mkdir checking for bash... /bin/sh Unknown MacOS X f90 compiler. Please add appropriate information to /Users/rob/Cactus/lib/make/known-architectures/darwin and send the updated file to CactusMaint We will try anyway ... checking whether the Fortran compiler (gfortran ) works... no configure: error: installation or configuration problem: Fortran compiler cannot create executables (see configs/sim/config-data/config.log for details).
Error reconfiguring sim-config make: *** [sim-config] Error 2
As you can see I get an error where it does not like the fortran
compiler.
I have tried all of the precursor stuff a number of times using both MacPorts and Homebrew and this does not seem to give any errors when installing.
I seem to be going round in circles to resolve this, if you are able to help that would be really appreciated.
Rob
Yours, Roland
-- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu .
Hello Bob,
I believe that I had previously done everything required and followed all of the install instructions properly. But I have now gone through them all again and still have the same problem. I have attached the config file you mentioned but it doesn't seem to give any more details that are spooled in the Jupyter notebook when I run it.
Let me see. In you case it looks for just gfortran. This is admittedly a bit odd. On MacOS using homebrew or macports it should look for gfortran-13 or gfortran-mp-13 respectively.
I have seen issues with Macs that change their machine name since they get derive it from their WiFi IP address. So here's my suggestion:
* run hostname -f to find out your laptops (current) machine name
* compare to the output of `simfactory/bin/sim whoami` which should be similar
* look for the newest file simfactory/mdb/machines/*.ini . It should have quite a long name that looks similar to the output of hostname above
* if the file name differs (other than in having the .ini extension) then you laptop got a new name since you set up Cactus and you will need to re-run `simfactory/bin/sim setup-silent` once more. It should (just above the SUMMARY output) say something along the lines of:
Creating machine gdd6l52n-ofc.ncsa.illinois.edu from generic: machine gdd6l52n-ofc.ncsa.illinois.edu [/Users/rhaas/ET_Next/repos/simfactory2/mdb/machines/gdd6l52n-ofc.ncsa.illinois.edu.ini] created successfully
* take a look at the ini file mentioned, and look for the "optionlist" entry. There should be a file of that name in simfactory/mdb/optionlists and that should contain the correct gfortran in its F90 entry
If you laptop does indeed change names, you can force simfactory to use a specific name by creating a file $HOME/.hostname and writing the desired machine name to it (eg gdd6l52n-ofc.ncsa.illinois.edu in my example above). You can also try and pass `--machine gdd6l52n-ofc.ncsa.illinois.edu` (for example) to each simfactory command which has the same effect (or at least should).
If any of these things turn out to be not true, could you include the full output from `setup-silent` (text, not a screenshot please) as well as the ini file and cfg files (machine definition and option list), please?
Also which package manager you are using (homebrew or macports) as well as the output from `which gfortran-13` or `which gfortran-mp-13` as appropriate both from within a Terminal and from withint the jupyter notebook (in a %%bash cell or using !).
Finally of course, sometimes the easiest way to clear out mysterious errors is to wipe Cactus (`rm -rf ~/Cactus`) and start from scratch (so that no lingering options are left behind).
Yours, Roland
Hi Roland,
Thanks for all of your help on this. I'm still failing dismally. I have made some notes against yours below and attached relevant files.
On Mon, 7 Aug 2023 at 16:27, Roland Haas rhaas@illinois.edu wrote:
Hello Bob,
I believe that I had previously done everything required and followed all of the install instructions properly. But I have now gone through them
all
again and still have the same problem. I have attached the config file you mentioned but it doesn't seem to give any more details that are spooled in the Jupyter notebook when I run it.
Let me see. In you case it looks for just gfortran. This is admittedly a bit odd. On MacOS using homebrew or macports it should look for gfortran-13 or gfortran-mp-13 respectively.
I have seen issues with Macs that change their machine name since they get derive it from their WiFi IP address. So here's my suggestion:
- run hostname -f to find out your laptops (current) machine name
Robs-Mac-mini.local
- compare to the output of `simfactory/bin/sim whoami` which should be similar
Current machine: Robs-Mac-mini.local
- look for the newest file simfactory/mdb/machines/*.ini . It should have quite a long name that looks similar to the output of hostname above
INI file attached below::::: The name is exactly the same
- if the file name differs (other than in having the .ini extension) then you laptop got a new name since you set up Cactus and you will need to re-run `simfactory/bin/sim setup-silent` once more. It should (just above the SUMMARY output) say something along the lines of:
Creating machine gdd6l52n-ofc.ncsa.illinois.edu from generic: machine gdd6l52n-ofc.ncsa.illinois.edu [/Users/rhaas/ET_Next/repos/simfactory2/mdb/machines/gdd6l52n-ofc.ncsa.illinois.edu.ini] created successfully
- take a look at the ini file mentioned, and look for the "optionlist" entry. There should be a file of that name in simfactory/mdb/optionlists and that should contain the correct gfortran in its F90 entry
The optionlist mentioned is : optionlist = generic.cfg I have also attached this optionlist. It refers to F90 = gfortran .
If you laptop does indeed change names, you can force simfactory to use a specific name by creating a file $HOME/.hostname and writing the desired machine name to it (eg gdd6l52n-ofc.ncsa.illinois.edu in my example above). You can also try and pass `--machine gdd6l52n-ofc.ncsa.illinois.edu` (for example) to each simfactory command which has the same effect (or at least should).
If any of these things turn out to be not true, could you include the full output from `setup-silent` (text, not a screenshot please) as well as the ini file and cfg files (machine definition and option list), please?
Also which package manager you are using (homebrew or macports) as well as the output from `which gfortran-13` /opt/homebrew/bin/gfortran-13or `which gfortran-mp-13` gfortran-mp-13 not found as
appropriate both from within a Terminal and from withint the jupyter
notebook (in a %%bash cell or using !). (*/opt/homebrew/bin/gfortran-13* and *gfortran-mp-13 not found* respectively)
II originally used MacPorts but when this failed I did the Homebrew stuff as well. Is this okay or will this now have led to some conflicts?
Finally of course, sometimes the easiest way to clear out mysterious errors is to wipe Cactus (`rm -rf ~/Cactus`) and start from scratch (so that no lingering options are left behind).
I tried this and had the same problem.
I have also now tried installing VMWare and creating an Ubuntu virtual machine but I could not get Jupyter Notebook to install on my 65bitArm version and my shell experience is really patchy. I feel like I've just turned up at medical school and have been given a heart transplant to perform!!!
I think my biggest problem here is my understanding of the underling stuff. I've programmed for years but in C#, Java, Python etc so rarely get my hands dirty in the back-end. I suspect I need to remove/uninstall some more stuff and start again but wouldn't know where to start with this. I've only been running this new Mac-mini for a few months so if I felt I had a good chance of success I would be tempted to do a full clean re-install of Ventura since all of my data is cloud backed.
Yours, Roland
-- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu .
Hello Rob,
Thanks for all of your help on this. I'm still failing dismally. I have made some notes against yours below and attached relevant files.
Thank you.
I have seen issues with Macs that change their machine name since they get derive it from their WiFi IP address. So here's my suggestion:
- run hostname -f to find out your laptops (current) machine name
Robs-Mac-mini.local
- compare to the output of `simfactory/bin/sim whoami` which should be similar
Current machine: Robs-Mac-mini.local
Ok, that all looks ok to me.
INI file attached below::::: The name is exactly the same
That would also be ok.
The optionlist mentioned is : optionlist = generic.cfg I have also attached this optionlist. It refers to F90 = gfortran .
Very strange. The only way that, on a mac, I could think of ending up with a setup like this would be if one had run
simfactory/bin/sim setup-silent
before having installed gfortran and gcc from homebrew or machports. Or really having run the command when say gcc-13 was not in $PATH.
Note that running
simfactory/bin/sim setup-silent
*then* installing macport and running
simfactory/bin/sim setup-silent
will do you no good. You have to first remove the ini file robs-mac-mini.local.ini (or the whole Cactus tree of course), otherwise simfactory treats your mac mini as a "known machine" and does not generate a ini file for it (and instead uses the existing one).
Though, with Homebrew, there actually is a gfortran file installed by Homebrew that is (at least for me) in $PATH and should be usable.
appropriate both from within a Terminal and from withint the jupyter
notebook (in a %%bash cell or using !). (*/opt/homebrew/bin/gfortran-13* and *gfortran-mp-13 not found* respectively)
Ok, so something is messed up with the Homebrew and MacPorts install since they did not add their "bin" directories to $PATH. Not sure why.
You can manually edit generic.cfg and instead of just having
F90 = gfortran
add the full path, so something like
F90 = /opt/homebrew/bin/gfortran
and similar for the other compilers (so that it does *not* use Apple's clang-in-gcc-disguise in /usr/bin).
This may help. Note that generic.cfg is part of the git checkout, so a git pull in simfactory2 will net you conflicts.
II originally used MacPorts but when this failed I did the Homebrew stuff as well. Is this okay or will this now have led to some conflicts?
Could be ok, though mixing those two can cause trouble in case some libraries and tools are used from one and some from the other. Then adding eg conda to the mix would tend to make things even worse.
I have also now tried installing VMWare and creating an Ubuntu virtual machine but I could not get Jupyter Notebook to install on my 65bitArm version and my shell experience is really patchy. I feel like I've just turned up at medical school and have been given a heart transplant to perform!!!
Yes, that would seem too much effort. Really it should work. My guess would be that you may have (wisely) avoided adding any of Homebrew's or MacPort's bin directories to your $PATH and this is the source of the problem. You could try this by removing the ini file, adding eg Homebrew's bin to PATH in a Terminal and running simfactory/bin/sim setup-silent and sim build in that terminal. If that works, then you have a way to make things work and have to decide on a way to switch between Homebrew and non-homebrew setups depending on what you would like to do.
I think my biggest problem here is my understanding of the underling stuff. I've programmed for years but in C#, Java, Python etc so rarely get my hands dirty in the back-end. I suspect I need to remove/uninstall some more stuff and start again but wouldn't know where to start with this. I've only been running this new Mac-mini for a few months so if I felt I had a good chance of success I would be tempted to do a full clean re-install of Ventura since all of my data is cloud backed.
Simfactory is a wrapper around (among other things) the Cactus build system. With the cfg files being option list files as described in the Cactus user guide:
http://einsteintoolkit.org/usersguide/UsersGuide.html#x1-18000B2
which are (almost) makefile fragments (though they are first parsed by Cactus so you cannot use arbitrary make constructs in them, eg variable expansion using $(FOO) does not work).
Yours, Roland
Are you running on the tutorial server or some other machine? It looks like you have a bad/missing gfortran.
--Steve
On 8/5/2023 6:49 AM, Rob wrote:
Hi,
I hope someone can help. I have tried to install the Einstein Toolkit but am getting an error in the final part of the process on the Jupyter CactusTutorial:
%%bash ./simfactory/bin/sim build -j2 --thornlist thornlists/einsteintoolkit.th http://einsteintoolkit.th
Output is:
Using configuration: sim Reconfiguring sim Writing configuration to: /Users/rob/Cactus/configs/sim/OptionList Cactus - version: 4.14.0 Reconfiguring sim. Using configuration options from configure line Setting fds to '3,5 -j --' End of options from configure line Adding configuration options from '/Users/rob/Cactus/configs/sim/OptionList'... Setting VERSION to '2018-12-13' Setting CPP to 'cpp' Setting CC to 'gcc' Setting CXX to 'g++' Setting FPP to 'cpp' Setting F90 to 'gfortran' Setting CPPFLAGS to '' Setting FPPFLAGS to '-traditional' Setting CFLAGS to '-g -std=gnu99' Setting CXXFLAGS to '-g -std=gnu++11' Setting F90FLAGS to '-g -fcray-pointer -ffixed-line-length-none' Setting LDFLAGS to '-rdynamic' Setting DEBUG to 'no' Setting CPP_DEBUG_FLAGS to '' Setting C_DEBUG_FLAGS to '' Setting CXX_DEBUG_FLAGS to '' Setting OPTIMISE to 'yes' Setting CPP_OPTIMISE_FLAGS to '' Setting C_OPTIMISE_FLAGS to '-O2' Setting CXX_OPTIMISE_FLAGS to '-O2' Setting F90_OPTIMISE_FLAGS to '-O2' Setting PROFILE to 'no' Setting CPP_PROFILE_FLAGS to '' Setting C_PROFILE_FLAGS to '-pg' Setting CXX_PROFILE_FLAGS to '-pg' Setting F90_PROFILE_FLAGS to '-pg' Setting WARN to 'yes' Setting CPP_WARN_FLAGS to '-Wall' Setting C_WARN_FLAGS to '-Wall' Setting CXX_WARN_FLAGS to '-Wall' Setting F90_WARN_FLAGS to '-Wall' Setting OPENMP to 'yes' Setting CPP_OPENMP_FLAGS to '-fopenmp' Setting FPP_OPENMP_FLAGS to '-D_OPENMP' Setting C_OPENMP_FLAGS to '-fopenmp' Setting CXX_OPENMP_FLAGS to '-fopenmp' Setting F90_OPENMP_FLAGS to '-fopenmp' Setting VECTORISE to 'yes' Setting VECTORISE_ALIGNED_ARRAYS to 'no' Setting VECTORISE_INLINE to 'yes' Setting PTHREADS_DIR to 'NO_BUILD' End of options from '/Users/rob/Cactus/configs/sim/OptionList'. creating cache ./config.cache checking host system type... x86_64-apple-darwin22.5.0 checking for mawk... no checking for gawk... no checking for nawk... no checking for awk... awk checking whether make sets ${MAKE}... yes checking whether the C compiler (gcc -g -std=gnu99 -rdynamic) works... yes checking whether the C compiler (gcc -g -std=gnu99 -rdynamic) is a cross-compiler... no checking whether we are using GNU C... yes checking whether the C++ compiler (g++ -g -std=gnu++11 -rdynamic) works... yes checking whether the C++ compiler (g++ -g -std=gnu++11 -rdynamic) is a cross-compiler... no checking whether we are using GNU C++... yes checking for nvcc... no checking for ranlib... ranlib checking for perl... perl checking for gtar... no checking for tar... tar checking for xargs... xargs checking for gzip... gzip checking for gpatch... no checking for patch... patch checking for git... git checking for ar... ar checking for mkdir... mkdir checking for bash... /bin/sh Unknown MacOS X f90 compiler. Please add appropriate information to /Users/rob/Cactus/lib/make/known-architectures/darwin and send the updated file to CactusMaint We will try anyway ... checking whether the Fortran compiler (gfortran ) works... no configure: error: installation or configuration problem: Fortran compiler cannot create executables (see configs/sim/config-data/config.log for details).
Error reconfiguring sim-config make: *** [sim-config] Error 2 As you can see I get an error where it does not like the fortran compiler. I have tried all of the precursor stuff a number of times using both MacPorts and Homebrew and this does not seem to give any errors when installing. I seem to be going round in circles to resolve this, if you are able to help that would be really appreciated. Rob
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Steven R. Brandt