16 Jun
2020
16 Jun
'20
10:47 a.m.
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
16 Jun
16 Jun
2:50 p.m.
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.de<mailto:r.deepu@fz-juelich.de>
Institute for Advanced Simulation http://www.fz-juelich.de/ias/jsc
Forschungszentrum Jülich GmbH
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------------------------------------------------------------------------------------------------
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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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
3:08 p.m.
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(a)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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Rajalekshmi Deepu
Simulation Lab Neuroscience
Division HPC in Neuroscience Phone: +49 2461 61 8945
Jülich Supercomputing Centre (JSC) E-mail: r.deepu(a)fz-juelich.de
Institute for Advanced Simulation http://www.fz-juelich.de/ias/jsc
Forschungszentrum Jülich GmbH
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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
------------------------------------------------------------------------------------------------
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17 Jun
17 Jun
11:54 a.m.
Lekshmi,
Is there a way to determine it by using a command?
On Tue, Jun 16, 2020 at 21:50 Rajalekshmi Deepu <r.deepu(a)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[image: Inline image]
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Rajalekshmi Deepu
Simulation Lab Neuroscience
Division HPC in Neuroscience Phone: +49 2461 61 8945
Jülich Supercomputing Centre (JSC) E-mail: r.deepu(a)fz-juelich.de
Institute for Advanced Simulation http://www.fz-juelich.de/ias/jsc
Forschungszentrum Jülich GmbH
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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
------------------------------------------------------------------------------------------------
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18 Jun
18 Jun
12:06 p.m.
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 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(a)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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Rajalekshmi Deepu
Simulation Lab Neuroscience
Division HPC in Neuroscience Phone: +49 2461 61 8945
Jülich Supercomputing Centre (JSC) E-mail: r.deepu(a)fz-juelich.de
Institute for Advanced Simulation http://www.fz-juelich.de/ias/jsc
Forschungszentrum Jülich GmbH
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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12:18 p.m.
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(a)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:
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(a)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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Rajalekshmi Deepu
Simulation Lab Neuroscience
Division HPC in Neuroscience Phone: +49 2461 61 8945
Jülich Supercomputing Centre (JSC) E-mail: r.deepu(a)fz-juelich.de
Institute for Advanced Simulation http://www.fz-juelich.de/ias/jsc
Forschungszentrum Jülich GmbH
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
_______________________________________________
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_______________________________________________
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11:38 p.m.
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,
Is there a way to determine it by using a command?
On Tue, Jun 16, 2020 at 21:50 Rajalekshmi Deepu <r.deepu(a)fz-juelich.de
<mailto: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:
--
Rajalekshmi Deepu
Simulation Lab Neuroscience
Division HPC in Neuroscience Phone: +49 2461 61 8945
Jülich Supercomputing Centre (JSC) E-mail: r.deepu(a)fz-juelich.de
Institute for Advanced Simulation http://www.fz-juelich.de/ias/jsc
Forschungszentrum Jülich GmbH
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,
PetiaInline image
_______________________________________________
NEST Users mailing list --users(a)nest-simulator.org
<mailto:users@nest-simulator.org>
To unsubscribe send an email tousers-leave(a)nest-simulator.org
<mailto:users-leave@nest-simulator.org>
--
Rajalekshmi Deepu
Simulation Lab Neuroscience
Division HPC in Neuroscience Phone: +49 2461 61 8945
Jülich Supercomputing Centre (JSC) E-mail:r.deepu@fz-juelich.de
<mailto:r.deepu@fz-juelich.de>
Institute for Advanced Simulationhttp://www.fz-juelich.de/ias/jsc
Forschungszentrum Jülich GmbH
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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<mailto:users@nest-simulator.org>
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<mailto:users-leave@nest-simulator.org>
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19 Jun
19 Jun
10:10 a.m.
Lekshmi,
On Thu, Jun 18, 2020 at 11:38:02PM +0200, Rajalekshmi Deepu 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
[...]
"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 ...
On 17.06.20 11:54, Itaru Kitayama wrote:
>Lekshmi,
>
>Is there a way to determine it by using a command?
... 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
1:23 p.m.
Dear Petia,
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.
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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
1:25 p.m.
Thank you very much!Best wishes,Petia
On Friday, June 19, 2020, 2:23:29 PM GMT+3, Jochen Martin Eppler
<j.eppler(a)fz-juelich.de> wrote:
Dear Petia,
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.
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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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1:46 p.m.
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
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10 comments
5 participants
participants (5)
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Harold Gutch -
Itaru Kitayama -
Jochen Martin Eppler -
Petia Koprinkova -
Rajalekshmi Deepu