Hello, I am new to the Einstein toolkit, so I wanted to go through the tutorial first. Unfortunately, I do not get beyond the step of building the Einstein toolkit: %%bash ./simfactory/bin/sim build -j2 --thornlist thornlists/einsteintoolkit.th
I attached the output as a text file due to its length. The output ends with: /usr/bin/ld: /usr/local/lib/../lib/libadios2_cxx11_mpi.so.2.10: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[1]: *** [/home/j/Cactus/lib/make/make.configuration:150: /home/j/Cactus/exe/cactus_sim] Error 1 make: *** [Makefile:265: sim] Error 2
After this cell, I cannot proceed further since the executable "cactus_sim" was not created. The step of building the Einstein toolkit assumes that SimFactory has been set up successfully. The step for configuring it, %%bash ./simfactory/bin/sim setup-silent Gives the output:
Here we will define some necessary Simulation Factory defaults.
Determining local machine name: et-juphub
--------------------SUMMARY--------------------:
[default] user = j email = j allocation = NO_ALLOCATION
------------------END SUMMARY------------------:
Contents successfully written to /home/j/Cactus/repos/simfactory2/etc/defs.local.ini
I am running the web-based tutorial, so I thought just running the Jupyter notebook cells would suffice (I tried restarting the kernel, but this did not help). Do you know how I could resolve this error? Thank you very much for your help, and best wishes, Julia
Hello Julia,
I am new to the Einstein toolkit, so I wanted to go through the tutorial first. Unfortunately, I do not get beyond the step of building the Einstein toolkit: %%bash ./simfactory/bin/sim build -j2 --thornlist thornlists/einsteintoolkit.th
I attached the output as a text file due to its length. The output ends with: /usr/bin/ld: /usr/local/lib/../lib/libadios2_cxx11_mpi.so.2.10: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[1]: *** [/home/j/Cactus/lib/make/make.configuration:150: /home/j/Cactus/exe/cactus_sim] Error 1 make: *** [Makefile:265: sim] Error 2
Hmm, that is a linker error. My guess would be that one needs to explicitly list the C++ bindings for MPI in the linker library list.
This should of course work automatically, but clearly is not anymore.
I am running the web-based tutorial, so I thought just running the Jupyter notebook cells would suffice (I tried restarting the kernel, but this did not help).
In particular on the ET maintained tutorial server it should just work. Since it is not, we will have to fix the server and the code.
Do you know how I could resolve this error?
Let me try and see and get back to you.
Yours, Roland
Hello Julia,
Sorry for the delay, but this turned into a bit more of a rabbit hole than expected.
Please give this another try on the tutorial server. You will have to, unfortunately, start from scratch to get new versions of the simfactory machine description files.
If you like to you can also try and update only Simulation Factory using:
cd repos/simfactory2 git pull
then remove your configs/sim directory to force a compilation from scratch using the new files.
On you laptop things probably work fine, at least as long as there is no pro-compiled version of ADIOS2 installed already. On a cluster with ADIOS2 installed you may need to use branch rhaas/mpilibs of ExternalLibraries/ADIOS2 which we hope to very soon merge into ExternalLibraries/ADIOS2's master branch.
Please let me know if this solves the issue for you.
Just in case (though I suspect you are aware) there is the group of Philipp Moesta at UVA that uses the EinsteinToolkit extensively and may be able to provide some help as well.
Yours, Roland
Hello Julia,
I am new to the Einstein toolkit, so I wanted to go through the tutorial first. Unfortunately, I do not get beyond the step of building the Einstein toolkit: %%bash ./simfactory/bin/sim build -j2 --thornlist thornlists/einsteintoolkit.th
I attached the output as a text file due to its length. The output ends with: /usr/bin/ld: /usr/local/lib/../lib/libadios2_cxx11_mpi.so.2.10: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[1]: *** [/home/j/Cactus/lib/make/make.configuration:150: /home/j/Cactus/exe/cactus_sim] Error 1 make: *** [Makefile:265: sim] Error 2
Hmm, that is a linker error. My guess would be that one needs to explicitly list the C++ bindings for MPI in the linker library list.
This should of course work automatically, but clearly is not anymore.
I am running the web-based tutorial, so I thought just running the Jupyter notebook cells would suffice (I tried restarting the kernel, but this did not help).
In particular on the ET maintained tutorial server it should just work. Since it is not, we will have to fix the server and the code.
Do you know how I could resolve this error?
Let me try and see and get back to you.
Yours, Roland
users@lists.einsteintoolkit.org
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Julia Speicher -
Roland Haas -
Roland Haas