Hi everyone, I've been unsuccessfully trying to run the latest version of Einstein Toolkit on the Sciama HPC cluster where I have been using the 2020_05 version so far. Could someone please help? I have tried three different approaches and put the terminal output and config.log files of each in the folder here (too heavy for email)Compiling_ET_2023_11_on_Sciama - Google Drive as well as the Sciama config files I used in the B approach.
A) Using the config files already included in Einstein Toolkit, using intel_comp/2019.2 it gives the error Cactus requires a C++11 compiler -- check your C++ compiler and C++ compiler flags
If using g++ at least version 6 is required, if using icpc use -gxx-name to use libstc++ from g++ at least version 6 I tried using intel_comp/2020.1 (the latest available on Sciama) and got the same error (and some module warnings). I found the path to g++ and so tried to add -gxx-name = /opt/apps/compilers/gnu_comp/cfg/9.1.0/intel64/bin/g++ to CXXFLAGS in sciama.cfg but this didn't change anything. B) Using gnu_comp/13.2.0 instead, I changed modules and flags where you can see in the Google Drive folder the .ini and .cfg files I use. It compiles all the way to the part "Creating cactus_sim" where it lists all the thorns then I get lots of errors of the type patch_system.cc:(.text+0xbe): undefined reference to `H5open'
/usr/bin/ld: Dwarf Error: found dwarf version '1', this reader only handles version 2, 3 and 4 information. I have this message for lots of files .cc, .c, .f90 undefined reference to lots of different H5 functions (and also dsytrf_ dgetrf_ dgesv_ dsysv_ dposv_ dgbsv_) complaining about dwarf version 'any number'. The only other somewhat similar example I found of this online is here https://github.com/tinygo-org/tinygo/issues/1415%C2%A0but it's not that helpful. I'm guessing it's unhappy with hdf5, unfortunately, the latest version on Sciama is 1.10.5. Do I just need a later version of hdf5 or is this something else? C) I tried with the EinsteinToolkit hdf5 (that I see is version 1.12.0) with HDF5_DIR = BUILD and commented out HDF5_LIB_DIRS and HDF5_INC_DIRS, as it compiles it doesn't get as far. In the output, I'm under the impression it manages to build it properly, but later it seems to not be unable to find it, but it should just be within Einstein Toolkit right? Thank you for your help,Robyn
Hello Robyn, all,
Just responding here to "close" the conversation.
Robyn and I have had an offline discussion and I was able to help with higher level issue that was what triggered to attempt at using the newer release.
Yours, Roland
Hi everyone, I've been unsuccessfully trying to run the latest version of Einstein Toolkit on the Sciama HPC cluster where I have been using the 2020_05 version so far. Could someone please help? I have tried three different approaches and put the terminal output and config.log files of each in the folder here (too heavy for email)Compiling_ET_2023_11_on_Sciama - Google Drive as well as the Sciama config files I used in the B approach.
A) Using the config files already included in Einstein Toolkit, using intel_comp/2019.2 it gives the error Cactus requires a C++11 compiler -- check your C++ compiler and C++ compiler flags
If using g++ at least version 6 is required, if using icpc use -gxx-name to use libstc++ from g++ at least version 6 I tried using intel_comp/2020.1 (the latest available on Sciama) and got the same error (and some module warnings). I found the path to g++ and so tried to add -gxx-name = /opt/apps/compilers/gnu_comp/cfg/9.1.0/intel64/bin/g++ to CXXFLAGS in sciama.cfg but this didn't change anything. B) Using gnu_comp/13.2.0 instead, I changed modules and flags where you can see in the Google Drive folder the .ini and .cfg files I use. It compiles all the way to the part "Creating cactus_sim" where it lists all the thorns then I get lots of errors of the type patch_system.cc:(.text+0xbe): undefined reference to `H5open'
/usr/bin/ld: Dwarf Error: found dwarf version '1', this reader only handles version 2, 3 and 4 information. I have this message for lots of files .cc, .c, .f90 undefined reference to lots of different H5 functions (and also dsytrf_ dgetrf_ dgesv_ dsysv_ dposv_ dgbsv_) complaining about dwarf version 'any number'. The only other somewhat similar example I found of this online is here https://urldefense.com/v3/__https://github.com/tinygo-org/tinygo/issues/1415... but it's not that helpful. I'm guessing it's unhappy with hdf5, unfortunately, the latest version on Sciama is 1.10.5. Do I just need a later version of hdf5 or is this something else? C) I tried with the EinsteinToolkit hdf5 (that I see is version 1.12.0) with HDF5_DIR = BUILD and commented out HDF5_LIB_DIRS and HDF5_INC_DIRS, as it compiles it doesn't get as far. In the output, I'm under the impression it manages to build it properly, but later it seems to not be unable to find it, but it should just be within Einstein Toolkit right? Thank you for your help,Robyn
users@lists.einsteintoolkit.org
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Robyn Munoz -
Roland Haas