Hi, We are trying to install NEST on supercomputer Ahitohol but we were unable to manage with some errors. Here attached is a screenshot with last reported errors. Could you help to resolve it?Regards,Petia
Hi Petia,
Libraries like GLIBCXX_3.4.21 is part of gcc compiler. Do you have multiple versions of GCC compiler installed on the system?
For details about versions of gcc and versions of appropriate libstdc++, please take a look here:
https://gcc.gnu.org/onlinedocs/libstdc++/manual/abi.html
Best regards,
Lekshmi
On 16.06.20 10:47, Petia Koprinkova wrote: Hi,
We are trying to install NEST on supercomputer Ahitohol but we were unable to manage with some errors. Here attached is a screenshot with last reported errors.
Could you help to resolve it? Regards, Petia[Inline image]
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-- Rajalekshmi Deepu Simulation Lab Neuroscience Division HPC in Neuroscience Phone: +49 2461 61 8945 Jülich Supercomputing Centre (JSC) E-mail: r.deepu@fz-juelich.demailto:r.deepu@fz-juelich.de Institute for Advanced Simulation http://www.fz-juelich.de/ias/jsc Forschungszentrum Jülich GmbH
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Dear Lekshmi, Thank you very much! We have to check what version og gcc we have... Best,Petia
On Tuesday, June 16, 2020, 3:50:45 PM GMT+3, Rajalekshmi Deepu r.deepu@fz-juelich.de wrote:
Hi Petia,
Libraries like GLIBCXX_3.4.21 is part of gcc compiler. Do you have multiple versions of GCC compiler installed on the system?
For details about versions of gcc and versions of appropriate libstdc++, please take a look here:
https://gcc.gnu.org/onlinedocs/libstdc++/manual/abi.html
Best regards,
Lekshmi
On 16.06.20 10:47, Petia Koprinkova wrote:
Hi, We are trying to install NEST on supercomputer Ahitohol but we were unable to manage with some errors. Here attached is a screenshot with last reported errors. Could you help to resolve it?Regards,Petia
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Petia,
going by your output and the fact that you are mentioning a "supercomputer", my guess is that there are versions of gcc available as environment modules (i.e., as in "module load gcc/...") that are newer than the system base versions. I suspect you compiled NEST with such a gcc module loaded, but the module was *not* loaded when running "make installcheck".
The output of the "cmake" command (in the first step of building NEST) would be helpful here - but as that probably is no longer available, it might be helful to know what CMAKE_CXX_COMPILER and CMAKE_C_COMPILER are set to in CMakeCache.txt (this would be in the build directory, i.e., the directory you ran "cmake" and "make" in). I assume they are not set to /usr/bin/gcc and /usr/bin/g++ but point to some other directory.
Anyway, my guess based on your screenshot is that you merely need to load the correct gcc module to get it running.
cheers, Harold
On Tue, Jun 16, 2020 at 01:08:06PM +0000, Petia Koprinkova wrote:
Dear Harold, Thank yuo very much! I am forwarding your comments to the assistant responsible for installation.
Meanwhile I was wandering whether we will be able to run python code importing the NEST library on supercomputer? A colleague alredy said that there might be issue with python for NEST. Best,Petia
On Thursday, June 18, 2020, 1:07:14 PM GMT+3, Harold Gutch harold.gutch@ds.mpg.de wrote:
Petia,
going by your output and the fact that you are mentioning a "supercomputer", my guess is that there are versions of gcc available as environment modules (i.e., as in "module load gcc/...") that are newer than the system base versions. I suspect you compiled NEST with such a gcc module loaded, but the module was *not* loaded when running "make installcheck".
The output of the "cmake" command (in the first step of building NEST) would be helpful here - but as that probably is no longer available, it might be helful to know what CMAKE_CXX_COMPILER and CMAKE_C_COMPILER are set to in CMakeCache.txt (this would be in the build directory, i.e., the directory you ran "cmake" and "make" in). I assume they are not set to /usr/bin/gcc and /usr/bin/g++ but point to some other directory.
Anyway, my guess based on your screenshot is that you merely need to load the correct gcc module to get it running.
cheers, Harold
On Tue, Jun 16, 2020 at 01:08:06PM +0000, Petia Koprinkova wrote:
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Dear Petia,
we routinely run very large PyNEST simulations on supercomputers, so as long as all the other Python libraries you need are available, I don't see a problem here.
Cheers, Jochen!
-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation
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Thank you very much!Best wishes,Petia
On Friday, June 19, 2020, 2:23:29 PM GMT+3, Jochen Martin Eppler j.eppler@fz-juelich.de wrote:
Dear Petia,
we routinely run very large PyNEST simulations on supercomputers, so as long as all the other Python libraries you need are available, I don't see a problem here.
Cheers, Jochen!
-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
Petia,
On Thu, Jun 18, 2020 at 10:18:03AM +0000, Petia Koprinkova wrote:
Meanwhile I was wandering whether we will be able to run python code importing the NEST library on supercomputer? A colleague alredy said that there might be issue with python for NEST.
Well, some things of course depend on the way things are set up on your HPC system, but with "usual setups" it should work pretty much anywhere. You might have to keep a few peculiarities of your system in mind -- for example, if you indeed need to load a certain environment module in order for NEST to run, then this has to happen on the compute nodes where your job is run, too. In this case you will have to either propagate some settings from your local environment (things like PATH and LD_LIBRARY_PATH) to the compute nodes -- or (and this is what I would do), load the right modules in your job script(s).
The details will depend on your setup, installed software, used queuing system/resource manager and other parameters, but in general it should either work (almost) out of the box, or at most require only little addiitonal work.
Harold
Lekshmi,
Is there a way to determine it by using a command?
On Tue, Jun 16, 2020 at 21:50 Rajalekshmi Deepu r.deepu@fz-juelich.de wrote:
Dear Itaru,
You meant to check the GLIBCXX versions?
If yes, you could try the below sample command:
$ strings /lib64/libstdc++.so.6 | grep GLIBCXX GLIBCXX_3.4 GLIBCXX_3.4.1 GLIBCXX_3.4.2 GLIBCXX_3.4.3 GLIBCXX_3.4.4 GLIBCXX_3.4.5 GLIBCXX_3.4.6 GLIBCXX_3.4.7 GLIBCXX_3.4.8 GLIBCXX_3.4.9 GLIBCXX_3.4.10 GLIBCXX_3.4.11 GLIBCXX_3.4.12 GLIBCXX_3.4.13 GLIBCXX_3.4.14 GLIBCXX_3.4.15 GLIBCXX_3.4.16 GLIBCXX_3.4.17 GLIBCXX_3.4.18 GLIBCXX_3.4.19 GLIBCXX_DEBUG_MESSAGE_LENGTH
Best regards,
Lekshmi
On 17.06.20 11:54, Itaru Kitayama wrote:
Lekshmi,
On Thu, Jun 18, 2020 at 11:38:02PM +0200, Rajalekshmi Deepu wrote:
"objdump -p /lib64/libstdc++.so.6" will also print the GCC C++ APIs supported by your libstdc++ - if you want to parse that further automatically, piping it through awk seems to do the job:
objdump -p /usr/lib64/libstdc++.so.6 | awk '/^[0-9]/{print $NF}'
Technically "strings" can return false positives due to other string matches - even if, speaking practically, this is rather unlikely to happen.
It seems I misunderstood Kitayama-san's question, to me ...
... sounded like how to list all versions of GCC that are installed/available. "gcc -v" together with listing the available environment modules ("module list") might be helpful there, but that won't find GCC versions installed in your home directory (or similar) or modules that only become available once you load other modules. "module spider" has failed me so often in the past that at least *to me* it doesn't seem worth suggesting that.
cheers, Harold