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Re: MPI problem with e-prop tutorials
by Xavier Otazu Porter 31 Oct '25

31 Oct '25

Hi Camilo, Thanks a lot for your help ... but problem remains. Now I get: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 545, in <module> readout_signal = readout_signal.reshape((readout_signal[0], n_iter, batch_size, steps["sequence"])) #readout_signal = readout_signal.reshape((n_out, n_iter, batch_size, steps["sequence"])) TypeError: only integer scalar arrays can be converted to a scalar index Xavier ________________________________ From: Camilo Jara Do Nascimento <C.Jara-Do-Nascimento(a)sussex.ac.uk> Sent: Wednesday, October 29, 2025 4:56 PM To: NEST User Mailing List <users(a)nest-simulator.org>; Xavier Otazu Porter <xotazu(a)cvc.uab.cat> Subject: Re: [NEST Users] MPI problem with e-prop tutorials Hi Xavier, The problem I see is that the readout first dimension is based on the n_out, and when using mpi to parallelizing it will use this first dimension to parallelize your instances. I quickly fixed it by changing the first dimension to be readout_signal.shape[0] since its already defined before by using the "idc" indexes. readout_signal = readout_signal.reshape((readout_signal.shape[0], n_iter, batch_size, steps["sequence"])) Hope this helps. Best, Camilo Jara D. ________________________________ From: Xavier Otazu <xotazu(a)cvc.uab.cat> Sent: 29 October 2025 14:03 To: users(a)nest-simulator.org <users(a)nest-simulator.org> Subject: [NEST Users] MPI problem with e-prop tutorials Hello, I have tried to execute one of the e-prop tutorials (eprop_supervised_regression_handwriting_bsshslm_2020.py) and get into problems when activating MPI. I do not know whether it is an e-prop C++ implementation problem or a Python tutorial code problem (in some cases, but not all of them, it looks like the last one). I have two files (hostfile_orig_1 and hostfile_orig_2) to define in what nodes of the cluster to execute the program. The content of these files is: hostfile_orig_1: node0 slots=1 node1 slots=1 hostfile_orig_2: node0 slots=2 node0 slots=2 The 'slots' key tells how many (mpi) processes can be executed on a particular node. Depending on the number of processes, the errors are a bit different. In all the following examples, I use "total_num_virtual_procs": 2 on line 173 of tutorial file. Below I write the execution command and the output error. Command: mpirun -np 1 -hostfile hostfile_orig_1 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py Output: With a "serial" execution like this one, everything is OK: Command: mpirun -np 2 -hostfile hostfile_orig_2 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 404, in <module> nest.GetConnections(nrns_rec[0], nrns_rec[1:3]).set([params_init_optimizer] * 2) File "/home/neurobit/local/nest_3.9/lib64/python3.8/site-packages/nest/lib/hl_api_types.py", line 945, in set raise TypeError("status dict must be a dict, or a list of dicts of length {}".format(self.__len__())) TypeError: status dict must be a dict, or a list of dicts of length 1 Command: mpirun -np 2 -hostfile hostfile_orig_2 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py (commenting line 404) Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 545, in <module> readout_signal = readout_signal.reshape((n_out, n_iter, batch_size, steps["sequence"])) ValueError: cannot reshape array of size 364800 into shape (2,200,1,1824) Command: mpirun -np 2 -hostfile hostfile_orig_1 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py (commenting line 404) Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 545, in <module> readout_signal = readout_signal.reshape((n_out, n_iter, batch_size, steps["sequence"])) ValueError: cannot reshape array of size 364800 into shape (2,200,1,1824) Command: mpirun -np 4 -hostfile hostfile_orig_2 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py (commenting line 404 and using "total_num_virtual_procs": 4 on line 173 of tutorial file.) Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 493, in <module> "rec_out": get_weights(nrns_rec, nrns_out), File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 482, in get_weights conns["senders"] = np.array(conns["source"]) - np.min(conns["source"]) TypeError: tuple indices must be integers or slices, not str In this last case, program stops and hungs. If you want, I could submit a bug report on github. Xavier _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org Computer Vision Center<http://www.cvc.uab.cat> CONFIDENTIALITY WARNING<http://www.cvc.uab.es/?page_id=7475>

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SynapseCollection.get() causes overhead
by M. Maurycy Miękus 29 Oct '25

29 Oct '25

Hello, I am trying to access the list of approx. 13 000 000 synapses in my network. However, accessing any of the values in SynapseCollection runs longer than my whole simulation and can cause out of memory issues. In the following snippet, just the `conns.get('weight')` line takes my computer 13 minutes to compute and uses over 5 GB of memory, even though the data I am interested in should not be larger than 50 MB. importnest neurons= nest.Create('iaf_psc_exp', 20000) conn_dict= {'rule': 'fixed_indegree', 'indegree': 300} nest.Connect(neurons, neurons, conn_dict, syn_spec={'weight': 1.0}) conns= nest.GetConnections() conns.get('weight') How should I efficiently access/export the `source`, `target`, `weight` and `distance` synaptic variables without unnecessary time or memory overhead? Thank you. Best regards, Maurycy Miękus

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MPI problem with e-prop tutorials
by Xavier Otazu 29 Oct '25

29 Oct '25

Hello, I have tried to execute one of the e-prop tutorials (eprop_supervised_regression_handwriting_bsshslm_2020.py) and get into problems when activating MPI. I do not know whether it is an e-prop C++ implementation problem or a Python tutorial code problem (in some cases, but not all of them, it looks like the last one). I have two files (hostfile_orig_1 and hostfile_orig_2) to define in what nodes of the cluster to execute the program. The content of these files is: hostfile_orig_1: node0 slots=1 node1 slots=1 hostfile_orig_2: node0 slots=2 node0 slots=2 The 'slots' key tells how many (mpi) processes can be executed on a particular node. Depending on the number of processes, the errors are a bit different. In all the following examples, I use "total_num_virtual_procs": 2 on line 173 of tutorial file. Below I write the execution command and the output error. Command: mpirun -np 1 -hostfile hostfile_orig_1 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py Output: With a "serial" execution like this one, everything is OK: Command: mpirun -np 2 -hostfile hostfile_orig_2 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 404, in <module> nest.GetConnections(nrns_rec[0], nrns_rec[1:3]).set([params_init_optimizer] * 2) File "/home/neurobit/local/nest_3.9/lib64/python3.8/site-packages/nest/lib/hl_api_types.py", line 945, in set raise TypeError("status dict must be a dict, or a list of dicts of length {}".format(self.__len__())) TypeError: status dict must be a dict, or a list of dicts of length 1 Command: mpirun -np 2 -hostfile hostfile_orig_2 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py (commenting line 404) Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 545, in <module> readout_signal = readout_signal.reshape((n_out, n_iter, batch_size, steps["sequence"])) ValueError: cannot reshape array of size 364800 into shape (2,200,1,1824) Command: mpirun -np 2 -hostfile hostfile_orig_1 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py (commenting line 404) Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 545, in <module> readout_signal = readout_signal.reshape((n_out, n_iter, batch_size, steps["sequence"])) ValueError: cannot reshape array of size 364800 into shape (2,200,1,1824) Command: mpirun -np 4 -hostfile hostfile_orig_2 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py (commenting line 404 and using "total_num_virtual_procs": 4 on line 173 of tutorial file.) Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 493, in <module> "rec_out": get_weights(nrns_rec, nrns_out), File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 482, in get_weights conns["senders"] = np.array(conns["source"]) - np.min(conns["source"]) TypeError: tuple indices must be integers or slices, not str In this last case, program stops and hungs. If you want, I could submit a bug report on github. Xavier

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simulation control from a gui
by Peter Mason 20 Oct '25

20 Oct '25

I have a GUI to control and analyse the data from the simulation and it's parameters which uses shared memory to manage the state of the simulation and pass the data to the recipients. It seemed like a good idea to have a simulation restart button to normalise the start position and eventually have more than a single independent simulation. This would require the simulation to run independently of the GUI which up to this point it did not. To implement this I tried running the simulation code in a separate thread having forgotten that Nest is not tread safe and it crashed. The simulation code including Nest currently runs in multiple processes. Before attempting to do it myself i asked CoPilot to produce the code attached which I do not understand in detail but this is normal because it uses python features of which I have no knowledge. Up to now. The code runs apart from some 'hopefully simple' details of the button control lost in this conversion Is this application of interest? Is there a standard way to do this?

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Open NEST Developer Video Conference Monday October 20, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 20 Oct '25

20 Oct '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday October 20, at 11:30 CEST (UTC+0200).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2025-10-20-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-10-20-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 <https://conf.dfn.de/webapp/conference/97938800> * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you’re in. In case you see a dfnconf logo and the phrase “Auf den Meetingveranstalter warten”, just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. * Using the H.323 protocol (eg Polycom): |vc.dfn.net##97938800| or |194.95.240.2##97938800| * Using the SIP protocol:97938800@vc.dfn.de <mailto:97938800@vc.dfn.de> * By telephone: |+49-30-200-97938800| For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ --------------------------------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ---------------------------------------------------------------------------------------------

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Re: NEST Users Digest, Vol 79, Issue 2
by M. Maurycy Miękus 16 Oct '25

16 Oct '25

Dear Hans, Thank you for your response. Yes, I could be interested in contributing. Best regards, Maurycy On 15/10/2025 14:18, users-request(a)nest-simulator.org wrote: > Send NEST Users mailing list submissions to > users(a)nest-simulator.org > > To subscribe or unsubscribe via email, send a message with subject or > body 'help' to > users-request(a)nest-simulator.org > > You can reach the person managing the list at > users-owner(a)nest-simulator.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of NEST Users digest..." > > Today's Topics: > > 1. Re: SynapseCollection.get() causes overhead > (Hans Ekkehard Plesser) > > _______________________________________________ > 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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Open NEST Developer Video Conference Monday October 06 at 11:30 CEST (UTC+0200)
by Jessica Mitchell 06 Oct '25

06 Oct '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday October 06 at 11:30 CEST (UTC+0200).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. Agenda 1. Welcome 2. Review of NEST User Mailing List <https://www.nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simul…> 3. Project team <https://github.com/nest/nest-simulator/projects> round 4. In-depth discussion * #3582 > release 3.9! * Report from NEST tutorials The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2025-10-06-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Jessica Mitchell > *Log-in information* >> >> We use a virtual conference room provided by DFN >> <https://www.dfn.de/en/> (Deutsches Forschungsnetz). >> >> You can use the web client to connect. We however encourage everyone >> to use a headset for better audio quality or even a proper video >> conferencing system (see below) or software when available. >> >> >> Web client >> >> * Visit https://conf.dfn.de/webapp/conference/97938800 >> <https://conf.dfn.de/webapp/conference/97938800> >> * Enter your name and allow your browser to use camera and microphone >> * The conference does not need a PIN to join, just click join and >> you’re in. >> >> In case you see a dfnconf logo and the phrase “Auf den >> Meetingveranstalter warten”, just be patient, the meeting host needs >> to join first (a voice will tell you). >> >> >> VC system/software >> >> How to log in with a video conferencing system, depends on you VC >> system or software. >> >> * Using the H.323 protocol (eg Polycom): |vc.dfn.net##97938800| or >> |194.95.240.2##97938800| >> * Using the SIP protocol:97938800@vc.dfn.de <mailto:97938800@vc.dfn.de> >> * By telephone: |+49-30-200-97938800| >> >> For those who do not have a video conference system or suitable >> software, Polycom provides a pretty good free app for iOS and >> Android, so you can join from your tablet (Polycom RealPresence >> Mobile, available from AppStore/PlayStore). Note that firewalls may >> interfere with videoconferencing in various and sometimes confusing ways. >> >> For more technical information on logging in from various VC systems, >> please see >> >> http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4 >> <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> >> -- -------------------------- Dr. Jessica Mitchell (she/her) Documentation Specialist for Research Software Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institut Brain Structure-Function Relationships (INM-10) Jülich Research Centre and JARA Jülich, Germany Email:j.mitchell@fz-juelich.de Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers

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NEST 3.9 released
by Hans Ekkehard Plesser 25 Sep '25

25 Sep '25

Dear NEST Users, It is a great pleasure to annouce the release of NEST 3.9 which brings numerous improvements contributed by 24 developers through over 1200 commits to the NEST code base. Key enhancements include * Enhanced e-prop plasticity with biologically inspired features<https://github.com/nest/nest-simulator/pull/3207> * Re-organised tripartite connectivity generation to support multiple primary connection rules<https://github.com/nest/nest-simulator/pull/3204> * Windows docker instructions for installation<https://github.com/nest/nest-simulator/pull/3521> * Updates built-in timer documentation<https://github.com/nest/nest-simulator/pull/3490> * Extended detailed neuron documentation<https://github.com/nest/nest-simulator/pull/3448> * Enhanced gunicorn options in NEST Server<https://github.com/nest/nest-simulator/pull/3380> * Support for per-thread timers and timing MPI synchronization<https://github.com/nest/nest-simulator/pull/3378> * A logger for nest-server-mpi<https://github.com/nest/nest-simulator/pull/3365> and many bug fixes and code maintenance. I’d like to thank all who have contributed to making NEST 3.9 possible, in particular Jessica Mitchell who joined Dennis Terhorst in our release team and saw the completion of NEST 3.9—thanks a lot! Enjoy NEST 3.9! Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Research Committee Chair, Faculty of Science and Technology Head, Department of Data Science Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Open NEST Developer Video Conference Monday August 25, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 22 Sep '25

22 Sep '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday August 25, at 11:30 CEST (UTC+0200).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2025-08-25-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-08-25-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 <https://conf.dfn.de/webapp/conference/97938800> * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you’re in. In case you see a dfnconf logo and the phrase “Auf den Meetingveranstalter warten”, just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. * Using the H.323 protocol (eg Polycom): |vc.dfn.net##97938800| or |194.95.240.2##97938800| * Using the SIP protocol:97938800@vc.dfn.de <mailto:97938800@vc.dfn.de> * By telephone: |+49-30-200-97938800| For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ --------------------------------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ---------------------------------------------------------------------------------------------

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NEST Developers, please merge master to open PRs — Testsuite fix
by Hans Ekkehard Plesser 09 Sep '25

09 Sep '25

Dear NEST Developers, I have just merged PR #3569, which fixes slight glitches in the NEST testsuite. Please pull the newest master into all your open branches for pull requests to ensure that all test run. Note that PRs moving test from SLI to Py will from now on need to reduce the lower bound for the corresponding type of test (unit, regression, mpi) in testsuite/summarize_tests.py. Happy hacking! Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Research Committee Chair, Faculty of Science and Technology Head, Department of Data Science Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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