compiling browndye 2 on HPC
Gerald Keller
Hi Gary,
I am trying to compile browndye 2 on a HPC. For this I successfully installed ocaml 4.10.0, expat and apbs 3.0.0. Corresponding PATH and LD_LIBRARY_PATH variables were set. I am compiling on a SUSE Linux Enterprise Server 15 with gcc-11.2.0
I am able to build the aux-binaries but the bin-binaries fail due to (the very long expression is the lapack lib)
g++ obj/aux/scale_interactions.o -o bin/scale_interactions -L ./lib -lm -lpthread -lbrowndye -lexpat -Wl,--start-group /dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-mkl/2020.4.304-gcc-cmdxw76/mkl/lib/intel64/libmkl_intel_lp64.a /dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-mkl/2020.4.304-gcc-cmdxw76/mkl/lib/intel64/libmkl_intel_thread.a /dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-mkl/2020.4.304-gcc-cmdxw76/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -liomp5 -lpthread -lm -ldl
/usr/bin/ld: cannot find -lbrowndye
To get lapack working I had to change the LIB entry in the Makefile. So -llapack was replaced by $(MKL_LIB).
Do you have any idea how I could get this working?
Best regards,
Gerald
Robert Konecny
If the library (./lib/libbrowndye.a) was created in the previous step then
try replacing '-lbrowndye' with explicit path to it, e.g.
/your/path/browndye2/lib/libbrowndye.a.
Best,
Robert
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Gerald Keller
I checked for the browndye-lib, but it seems to fail when building it. Not sure if this is an expat issue (see build_err.log).
I attached build_all.log (stdout+stderr how it appears when compiling) build.log (stdout) and build_err.log (stderr). I hope this helps to identify what is going wrong.
Thanks for your assistance so far.
Best,
Gerald Keller
-----Ursprüngliche Nachricht-----
Von: Robert Konecny <r...@ucsd.edu>
Gesendet: Donnerstag, 14. April 2022 19:37
An: Gerald Keller <gerald...@uni-wuerzburg.de>
Cc: browndye...@ucsd.edu
Betreff: Re: compiling browndye 2 on HPC
Robert Konecny
Your log files look strange, the entries look out of order. Are using make
in parallel (make -j)? Can we see your makefile?
I understand why you are trying to use MKL but I would probably try first
to use the system BLAS/LAPACK (if installed) and see how that goes.
I'll try to reproduce what you are getting with Docker and SUSE later
today.
Best,
Robert
Robert Konecny
I can get it compiled with the system BLAS/LAPACK libraries on OpenSUSE
15.2 just fine. And with both g++ 7.5 and 10.2.
Best,
Robert
Gerald Keller
your question if I would use make -j XX all (I used make -j 20 all) made me to just try 'make all'. What shall I say, the building passed.
Do you have any idea, why the parallel make fails?
I then tried a test simulation on the HPC. When I executed 'we_simulation' it prompts me the Version of 28 Sep 2021, although I downloaded the source files a few days ago from here: https://browndye.ucsd.edu/downloads/browndye2.tar.gz
Would you please update the tarball to the latest version?
I then will let you know, if building and testing was successfully.
Best,
Gerald
Gesendet: Freitag, 15. April 2022 19:26
Robert Konecny
Good to hear you were able to finish the compilation!
It's interesting that your parallel make fails, though. Is this
reproducible, i.e. does it fail every time, even after running 'make
clean'? If yes, then there is some race condition in the make files which
is triggering this. I haven't see this yet, on any platform I have access
to.
The BrownDye version included in
https://browndye.ucsd.edu/downloads/browndye2.tar.gz is "BrownDye 2.0:
Version of 7 Mar 2022":
curl -s https://browndye.ucsd.edu/downloads/browndye2.tar.gz | tar xzO | grep Version
...
std::cout << "BrownDye 2.0: Version of 7 Mar 2022\n";
...
Perhaps you have older BrownDye executables in your PATH?
Best,
Robert