Return-Path: Received: from mx2.fz-rossendorf.de ([149.220.142.12] verified) by hzdr.de (CommuniGate Pro SMTP 6.1.11) with ESMTP id 14789387; Mon, 08 Aug 2016 18:14:48 +0200 Received: from localhost (localhost [127.0.0.1]) by mx2.fz-rossendorf.de (Postfix) with ESMTP id F379C45961; Mon, 8 Aug 2016 18:14:47 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at mx2.fz-rossendorf.de Authentication-Results: mx2.fz-rossendorf.de (amavisd-new); dkim=pass (2048-bit key) header.d=gmail.com Received: from mx2.fz-rossendorf.de ([127.0.0.1]) by localhost (mx2.fz-rossendorf.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id qAxYz7z5RnDy; Mon, 8 Aug 2016 18:14:43 +0200 (CEST) Received-SPF: Pass (sender SPF authorized) identity=mailfrom; client-ip=209.85.161.175; helo=mail-yw0-f175.google.com; envelope-from=djlexes@gmail.com; receiver=picongpu-users@hzdr.de Received: from mail-yw0-f175.google.com (mail-yw0-f175.google.com [209.85.161.175]) by mx2.fz-rossendorf.de (Postfix) with ESMTPS id 4C11C4595D; Mon, 8 Aug 2016 18:14:43 +0200 (CEST) Received: by mail-yw0-f175.google.com with SMTP id z8so307843004ywa.1; Mon, 08 Aug 2016 09:14:43 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:from:date:message-id:subject:to; bh=UmVEuSBn/2IFGK+a8+A3P6txL0GEqA6f568+n04KfoA=; b=gvyjZBrskekFvbTaXZFnndfahn5NHF2JhS6+nyYpu/tklrFSTy5CJI+i5KntAo+ZW2 Uo9j7uWxj2zgXKJuEGBVhDUiwBU/qpuq2p4Y/hVA8LspIgOn+w/VUYRO62SeSh+4mBCI f7oesLhgYWk3lsdP11/iOQowVlqlwlDMHVqKEZnw269B2w/+dTIohuqI42vzwAK2AB9C QK5MbJVp9dCpxvqR+wIbHHiNtS/5byp+tS73PaucXCicItpJk8d89BiUdPcNLqlcWfIR 70FpKAeCbtlVAyxJcja7vKHf1LrPrUl9okC9ihIzPBv+E2sAWycekXWb95YkmYYd4ihr 2iig== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:mime-version:in-reply-to:references:from:date :message-id:subject:to; bh=UmVEuSBn/2IFGK+a8+A3P6txL0GEqA6f568+n04KfoA=; b=a1YgX/geTDxHh73ogyoa600b6T6W6WK9f56kKXh4FPTZDMypqkBD2x4s/zVPX8qwQc 2VzOrtSg26U/PX1kGHLHEMA8o5pdoaohC4JCtnkOKBcGMqk0O514GEA89SUePjyAzBrD BSnA5fEcJTxuHErQaiKEIpV9G5DqogdiwkDF94uvjalnpJL2CiIOOIWtHS5dZ+Lot93L lhTTj9C8WO422lblYZMvYOI6623RYMN/2LAWKwH1lWmLWAeBaeW6di2nLpx7YGhLhLn2 dUuf1pxFHTBFiwmBB8maxVUheWsvzWQUDRBtR8Ze+g7PfATn4h5NV0BqxVWwMs02ixUM J2pQ== X-Gm-Message-State: AEkoouveLwjONNRV+9tKRCPBCEnBu7b3Mx+DKH/y75USoDu9DsXaHba150PpQzGsa7XaksgZOCk4SbU3YhOB3g== X-Received: by 10.129.146.200 with SMTP id j191mr68265834ywg.120.1470672881635; Mon, 08 Aug 2016 09:14:41 -0700 (PDT) MIME-Version: 1.0 Received: by 10.13.227.4 with HTTP; Mon, 8 Aug 2016 09:14:41 -0700 (PDT) In-Reply-To: References: From: Alex Francisco Date: Mon, 8 Aug 2016 11:14:41 -0500 Message-ID: Subject: Re: [PIConGPU-Users] Compiling splash2txt To: picongpu-users@hzdr.de, "Bussmann, Dr. Michael (FWKT) - 4167" , a.huebl@hzdr.de Content-Type: multipart/alternative; boundary=94eb2c08e196b0d7dc053991b616 --94eb2c08e196b0d7dc053991b616 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thank you very much this worked!!! When I do execute this line of code in my terminal show this: alex@alex-Satellite-L635:~/src/picongpu$ tbg -s qsub -c submit/0016gpus.cfg -t ~/paramSets/case001/submit/hypnos/k20_profile.tpl ~/runs/testBatch01/ The given cfg file "submit/0016gpus.cfg" does not exist (-c|--cfg). However, I turn to the folder case001 and there show me the folder testBatch01, I ask to yours, if it can be showing me this because I once create and do not need to recreate the subfolder (testBatch01) ?? alex@alex-Satellite-L635:~/runs$ ls testBatch01 and in the folder testBatch01 show me this files: alex@alex-Satellite-L635:~/runs/testBatch01$ ls picongpu tbg Furthermore, as I view the simulation output? I hope you can help me. Thank you very much. Alex Estupi=C3=B1=C3=A1n. 2016-08-06 11:33 GMT-05:00 Huebl, Axel : > I also fixed that compile problem in splash2txt by now. > > https://github.com/ComputationalRadiationPhysics/picongpu/pull/1545 > > You can just remove or comment out via "//" the line that is causing the > error. > > > Axel > > On 06.08.2016 11:07, Axel Huebl wrote: > > Dear Alex, > > > > You don't need to build the helper tool in post-processing, splash2txt > for now. Just skip step 6. > > > > Otherwise: please make sure the source code is unmodified. For compile > errors, please report compiler version, cmake version, cmake -L . output > and ubuntu version. > > > > Compile issues are also best tracked in our github since we can assign, > track, link and archive it there. > > > > Axel > > > > On August 6, 2016 10:56:09 AM EDT, "Bussmann, Dr. Michael (FWKT) - 4167= " > wrote: > >> Dear Alex, > >> > >> Could you please tell us which version of PIConGPU you are using, > >> provide CMake log files and CMakeLists.txt so we can have a look at > >> what > >> is going on. > >> > >> Best, Michael > >> > >> Am 05.08.2016 um 18:13 schrieb Alex Francisco: > >>> Dear Michael Bussmann and picongpu users: > >>> > >>> I appreciate your help, I already understood that ADIOS is optional, > >> but > >>> when i continue, my ubuntu terminal show me, the following error, > >> when I > >>> execute the step 6 "make -j": > >>> > >>> [ 50%] Building CXX object CMakeFiles/splash2txt.dir/splash2txt.cpp.o > >>> /home/alex/src/picongpu/src/tools/splash2txt/splash2txt.cpp: In > >> function > >>> =E2=80=98bool parseOptions(int, char**, ProgramOptions&)=E2=80=99: > >>> /home/alex/src/picongpu/src/tools/splash2txt/splash2txt.cpp:164:24: > >>> error: =E2=80=98desc=E2=80=99 was not declared in this scope > >>> errorStream << desc << "\n"; > >>> ^ > >>> CMakeFiles/splash2txt.dir/build.make:54: recipe for target > >>> 'CMakeFiles/splash2txt.dir/splash2txt.cpp.o' failed > >>> make[2]: *** [CMakeFiles/splash2txt.dir/splash2txt.cpp.o] Error 1 > >>> CMakeFiles/Makefile2:60: recipe for target > >>> 'CMakeFiles/splash2txt.dir/all' failed > >>> make[1]: *** [CMakeFiles/splash2txt.dir/all] Error 2 > >>> Makefile:117: recipe for target 'all' failed > >>> make: *** [all] Error 2 > >>> > >>> Im=C3=A1genes integradas 1 > >>> > >>> > >>> I hope you can help me. > >>> > >>> Thank you very much. > >>> > >>> Alex Estupi=C3=B1=C3=A1n. > >>> > >>> > >>> 2016-08-02 6:34 GMT-05:00 Bussmann, Dr. Michael (FWKT) - 4167 > >>> >: > >>> > >>> Oops, sorry, you completed step 5 and can go to step 6. My bad! > >>> > >>> Am 02.08.2016 um 13:25 schrieb Bussmann, Dr. Michael (FWKT) - > >> 4167: > >>> > Dear Alex, > >>> > > >>> > As Axel pointed out in his E-mail, this is no error. It simply > >>> tells you > >>> > that a software component is missing that is optional, but not > >>> required > >>> > to build PIConGPU. This means PIConGPU can use ADIOS, but does > >> not > >>> need > >>> > it to run properly. > >>> > > >>> > Yes, this is a bit confusing, but as you see the output tells > >> you that > >>> > your build files have been written to /home/alex/src/picongpu. > >> So > >>> > everything is fine! > >>> > > >>> > You have now completed step 6 in the install process, see here: > >>> > > >>> > >> https://github.com/ComputationalRadiationPhysics/ > picongpu/blob/release-0.1.2/doc/INSTALL.md > >>> > >> picongpu/blob/release-0.1.2/doc/INSTALL.md> > >>> > > >>> > As Axel also wrote, you can now simply go to step 7, typing > >> 'make'. > >>> > > >>> > If you run into problems, please provide error log files with > >> your > >>> > E-mails and keep posting to the Users mailing list. > >>> > > >>> > Hope this helps, Michael > >>> > > >>> > Am 02.08.2016 um 03:38 schrieb Alex Francisco: > >>> >> Dear Michael Bussmann: > >>> >> > >>> >> I hope you are well. I am a doctoral student at the University > >> of > >>> >> Colombia UIS. I am installing the PiconGpu program on my > >> laptop, my > >>> >> laptop has a software ubuntu 16.04 LTS 64-bit. > >>> >> > >>> >> My ubuntu terminal shows me the following error: > >>> >> > >>> >> -- Could NOT find ADIOS (missing: ADIOS_LIBRARIES > >>> ADIOS_INCLUDE_DIRS) > >>> >> (Required is at least version "1.6.0") > >>> >> > >>> >> > >>> >> Im=C3=A1genes integradas 1 > >>> >> > >>> >> > >>> >> the problem still, I am very interested in I can solve this > >>> problem. I > >>> >> need install this program for work in my doctoral job. > >>> >> > >>> >> I hope you can help me. > >>> >> > >>> >> Thank you very much. > >>> >> > >>> >> Alex Estupi=C3=B1=C3=A1n. > >>> >> > >>> > > >>> > ############################################################# > >>> > This message is sent to you because you are subscribed to > >>> > the mailing list >>> >. > >>> > To unsubscribe, E-mail to: >>> > > >>> > To switch to the DIGEST mode, E-mail to > >>> >> > > >>> > To switch to the INDEX mode, E-mail to > >>> >> > > >>> > Send administrative queries to >>> > > >>> > > >>> > >>> ############################################################# > >>> This message is sent to you because you are subscribed to > >>> the mailing list >>> >. > >>> To unsubscribe, E-mail to: >>> > > >>> To switch to the DIGEST mode, E-mail to > >>> >> > > >>> To switch to the INDEX mode, E-mail to > >> >>> > > >>> Send administrative queries to >>> > > >>> > >>> > >> > >> ############################################################# > >> This message is sent to you because you are subscribed to > >> the mailing list . > >> To unsubscribe, E-mail to: > >> To switch to the DIGEST mode, E-mail to > >> To switch to the INDEX mode, E-mail to > >> Send administrative queries to > > > > > > ############################################################# > > This message is sent to you because you are subscribed to > > the mailing list . > > To unsubscribe, E-mail to: > > To switch to the DIGEST mode, E-mail to > > To switch to the INDEX mode, E-mail to > > Send administrative queries to > > > > -- > > Axel Huebl > Phone +49 351 260 3582 > https://www.hzdr.de/crp > Computational Radiation Physics > Laser Particle Acceleration Division > Helmholtz-Zentrum Dresden - Rossendorf e.V. > > Bautzner Landstrasse 400, 01328 Dresden > POB 510119, D-01314 Dresden > Vorstand: Prof. Dr.Dr.h.c. R. Sauerbrey > Prof. Dr.Dr.h.c. P. Joehnk > VR 1693 beim Amtsgericht Dresden > > --94eb2c08e196b0d7dc053991b616 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
<= span class=3D"">Thank you very much this worked!!!

When I d= o execute this line of code in my terminal show this:

alex@alex-Sate= llite-L635:~/src/picongpu$ tbg -s qsub -c submit/0016gpus.cfg -t ~/paramSet= s/case001/submit/hypnos/k20_profile.tpl ~/runs/testBatch01/

The giv= en cfg file "submit/0016gpus.cfg" does not exist (-c|--cfg).
<= br>

However, I turn to the folder <= span id=3D"result_box" class=3D"" lang=3D"en">case001 and the= re show me the folder testBatch01, = I ask to yours, if it can be showing me this because I once= create and do not need to recreate the subfolder (te= stBatch01) <= span class=3D"">??

alex@alex-Satellite-L635:~/runs= $ ls
testBatch01

and in the folder testBatch01 show m= e this files:

alex@alex-Satellite-L635:~/runs/testBatch01$ l= s
picongpu=C2=A0 tbg


Furthermore, as I view the simulation output= ?


I hope you can help me.

= Thank you very much.

Alex Estupi=C3= =B1=C3=A1n.


2016-08-06 11:33 GM= T-05:00 Huebl, Axel <a.huebl@hzdr.de>:
I also fixed that compile problem in splash2txt by now.

=C2=A0 https://github.com/Co= mputationalRadiationPhysics/picongpu/pull/1545

You can just remove or comment out via "//" the line that is caus= ing the
error.


Axel

On 06.08.2016 11:07, Axel Huebl wrote:
> Dear Alex,
>
> You don't need to build the helper tool in post-processing, splash= 2txt for now. Just skip step 6.
>
> Otherwise: please make sure the source code is unmodified. For compile= errors, please report compiler version, cmake version, cmake -L . output a= nd ubuntu version.
>
> Compile issues are also best tracked in our github since we can assign= , track, link and archive it there.
>
> Axel
>
> On August 6, 2016 10:56:09 AM EDT, "Bussmann, Dr. Michael (FWKT) = - 4167" <m.bussmann@hzdr.de> wrote:
>> Dear Alex,
>>
>> Could you please tell us which version of PIConGPU you are using,<= br> >> provide CMake log files and CMakeLists.txt so we can have a look a= t
>> what
>> is going on.
>>
>> Best, Michael
>>
>> Am 05.08.2016 um 18:13 schrieb Alex Francisco:
>>> Dear Michael Bussmann and picongpu users:
>>>
>>> I appreciate your help, I already understood that ADIOS is opt= ional,
>> but
>>> when i continue, my ubuntu terminal show me, the following err= or,
>> when I
>>> execute the step 6 "make -j":
>>>
>>> [ 50%] Building CXX object CMakeFiles/splash2txt.dir/spla= sh2txt.cpp.o
>>> /home/alex/src/picongpu/src/tools/splash2txt/splash2txt.<= wbr>cpp: In
>> function
>>> =E2=80=98bool parseOptions(int, char**, ProgramOptions&)= =E2=80=99:
>>> /home/alex/src/picongpu/src/tools/splash2txt/splash2txt.<= wbr>cpp:164:24:
>>> error: =E2=80=98desc=E2=80=99 was not declared in this scope >>>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 errorStream << desc &l= t;< "\n";
>>>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0^
>>> CMakeFiles/splash2txt.dir/build.make:54: recipe for targe= t
>>> 'CMakeFiles/splash2txt.dir/splash2txt.cpp.o' fail= ed
>>> make[2]: *** [CMakeFiles/splash2txt.dir/splash2txt.cpp.o]= Error 1
>>> CMakeFiles/Makefile2:60: recipe for target
>>> 'CMakeFiles/splash2txt.dir/all' failed
>>> make[1]: *** [CMakeFiles/splash2txt.dir/all] Error 2
>>> Makefile:117: recipe for target 'all' failed
>>> make: *** [all] Error 2
>>>
>>> Im=C3=A1genes integradas 1
>>>
>>>
>>> I hope you can help me.
>>>
>>> Thank you very much.
>>>
>>> Alex Estupi=C3=B1=C3=A1n.
>>>
>>>
>>> 2016-08-02 6:34 GMT-05:00 Bussmann, Dr. Michael (FWKT) - 4167<= br> >>> <
m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de&= gt;>:
>>>
>>>=C2=A0 =C2=A0 =C2=A0Oops, sorry, you completed step 5 and can g= o to step 6. My bad!
>>>
>>>=C2=A0 =C2=A0 =C2=A0Am 02.08.2016 um 13:25 schrieb Bussmann, Dr= . Michael (FWKT) -
>> 4167:
>>>=C2=A0 =C2=A0 =C2=A0> Dear Alex,
>>>=C2=A0 =C2=A0 =C2=A0>
>>>=C2=A0 =C2=A0 =C2=A0> As Axel pointed out in his E-mail, thi= s is no error. It simply
>>>=C2=A0 =C2=A0 =C2=A0tells you
>>>=C2=A0 =C2=A0 =C2=A0> that a software component is missing t= hat is optional, but not
>>>=C2=A0 =C2=A0 =C2=A0required
>>>=C2=A0 =C2=A0 =C2=A0> to build PIConGPU. This means PIConGPU= can use ADIOS, but does
>> not
>>>=C2=A0 =C2=A0 =C2=A0need
>>>=C2=A0 =C2=A0 =C2=A0> it to run properly.
>>>=C2=A0 =C2=A0 =C2=A0>
>>>=C2=A0 =C2=A0 =C2=A0> Yes, this is a bit confusing, but as y= ou see the output tells
>> you that
>>>=C2=A0 =C2=A0 =C2=A0> your build files have been written to = /home/alex/src/picongpu.
>> So
>>>=C2=A0 =C2=A0 =C2=A0> everything is fine!
>>>=C2=A0 =C2=A0 =C2=A0>
>>>=C2=A0 =C2=A0 =C2=A0> You have now completed step 6 in the i= nstall process, see here:
>>>=C2=A0 =C2=A0 =C2=A0>
>>>
>> = https://github.com/ComputationalRadiationPhysics/picongpu/blob/re= lease-0.1.2/doc/INSTALL.md
>>>
>> <https://github.com/ComputationalRadiationPhysics/picongpu/blo= b/release-0.1.2/doc/INSTALL.md>
>>>=C2=A0 =C2=A0 =C2=A0>
>>>=C2=A0 =C2=A0 =C2=A0> As Axel also wrote, you can now simply= go to step 7, typing
>> 'make'.
>>>=C2=A0 =C2=A0 =C2=A0>
>>>=C2=A0 =C2=A0 =C2=A0> If you run into problems, please provi= de error log files with
>> your
>>>=C2=A0 =C2=A0 =C2=A0> E-mails and keep posting to the Users = mailing list.
>>>=C2=A0 =C2=A0 =C2=A0>
>>>=C2=A0 =C2=A0 =C2=A0> Hope this helps, Michael
>>>=C2=A0 =C2=A0 =C2=A0>
>>>=C2=A0 =C2=A0 =C2=A0> Am 02.08.2016 um 03:38 schrieb Alex Fr= ancisco:
>>>=C2=A0 =C2=A0 =C2=A0>> Dear Michael Bussmann:
>>>=C2=A0 =C2=A0 =C2=A0>>
>>>=C2=A0 =C2=A0 =C2=A0>> I hope you are well. I am a doctor= al student at the University
>> of
>>>=C2=A0 =C2=A0 =C2=A0>> Colombia UIS. I am installing the = PiconGpu program on my
>> laptop, my
>>>=C2=A0 =C2=A0 =C2=A0>> laptop has a software ubuntu 16.04= LTS 64-bit.
>>>=C2=A0 =C2=A0 =C2=A0>>
>>>=C2=A0 =C2=A0 =C2=A0>> My ubuntu terminal shows me the fo= llowing error:
>>>=C2=A0 =C2=A0 =C2=A0>>
>>>=C2=A0 =C2=A0 =C2=A0>> -- Could NOT find ADIOS (missing:= =C2=A0 ADIOS_LIBRARIES
>>>=C2=A0 =C2=A0 =C2=A0ADIOS_INCLUDE_DIRS)
>>>=C2=A0 =C2=A0 =C2=A0>> (Required is at least version &quo= t;1.6.0")
>>>=C2=A0 =C2=A0 =C2=A0>>
>>>=C2=A0 =C2=A0 =C2=A0>>
>>>=C2=A0 =C2=A0 =C2=A0>> Im=C3=A1genes integradas 1
>>>=C2=A0 =C2=A0 =C2=A0>>
>>>=C2=A0 =C2=A0 =C2=A0>>
>>>=C2=A0 =C2=A0 =C2=A0>> the problem still, I am very inter= ested in I can solve this
>>>=C2=A0 =C2=A0 =C2=A0problem. I
>>>=C2=A0 =C2=A0 =C2=A0>> need install this program for work= in my doctoral job.
>>>=C2=A0 =C2=A0 =C2=A0>>
>>>=C2=A0 =C2=A0 =C2=A0>> I hope you can help me.
>>>=C2=A0 =C2=A0 =C2=A0>>
>>>=C2=A0 =C2=A0 =C2=A0>> Thank you very much.
>>>=C2=A0 =C2=A0 =C2=A0>>
>>>=C2=A0 =C2=A0 =C2=A0>> Alex Estupi=C3=B1=C3=A1n.
>>>=C2=A0 =C2=A0 =C2=A0>>
>>>=C2=A0 =C2=A0 =C2=A0>
>>>=C2=A0 =C2=A0 =C2=A0> #################################= ############################
>>>=C2=A0 =C2=A0 =C2=A0> This message is sent to you because yo= u are subscribed to
>>>=C2=A0 =C2=A0 =C2=A0>=C2=A0 =C2=A0the mailing list <picongpu-users@hzdr.de
>>>=C2=A0 =C2=A0 =C2=A0<mailto:picongpu-users@hzdr.de>>.
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>>>=C2=A0 =C2=A0 =C2=A0<picongpu-users-digest@hzdr.de
>> <mailto:picong= pu-users-digest@hzdr.de>>
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>>>=C2=A0 =C2=A0 =C2=A0<picongpu-users-index@hzdr.de
>> <mailto:picongp= u-users-index@hzdr.de>>
>>>=C2=A0 =C2=A0 =C2=A0> Send administrative queries to=C2=A0 &= lt;picongpu-users-request= @hzdr.de
>>>=C2=A0 =C2=A0 =C2=A0<mailto:picongpu-users-request@hzdr.de>>
>>>=C2=A0 =C2=A0 =C2=A0>
>>>
>>>=C2=A0 =C2=A0 =C2=A0######################################= #######################
>>>=C2=A0 =C2=A0 =C2=A0This message is sent to you because you are= subscribed to
>>>=C2=A0 =C2=A0 =C2=A0 =C2=A0the mailing list <picongpu-users@hzdr.de
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>>
>> ############################################################<= wbr>#
>> This message is sent to you because you are subscribed to
>>=C2=A0 the mailing list <picongpu-users@hzdr.de>.
>> To unsubscribe, E-mail to: <picongpu-users-off@hzdr.de>
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--

Axel Huebl
Phone +49 = 351 260 3582
ht= tps://www.hzdr.de/crp
Computational Radiation Physics
Laser Particle Acceleration Division
Helmholtz-Zentrum Dresden - Rossendorf e.V.

Bautzner Landstrasse 400, 01328 Dresden
POB 510119, D-01314 Dresden
Vorstand: Prof. Dr.Dr.h.c. R. Sauerbrey
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Prof. Dr.Dr.h.c. P. Joehnk
VR 1693 beim Amtsgericht Dresden


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