opal AT lists.psi.ch

Subject: The OPAL Discussion Forum

List archive

Re: [Opal] mpirun H5WriteStepAttribFloat64

From: "Dr. Simon Friederich" <s.friederich AT uni-mainz.de>
To: <opal AT lists.psi.ch>
Subject: Re: [Opal] mpirun H5WriteStepAttribFloat64
Date: Mon, 5 Oct 2020 12:12:55 +0200
Authentication-results: localhost; iprev=pass (ironport-2.zdv.net) smtp.remote-ip=134.93.178.242; spf=pass smtp.mailfrom=uni-mainz.de; dkim=pass header.d=uni-mainz.de header.s=20190702 header.a=rsa-sha256; dmarc=pass header.from=uni-mainz.de
Ironport-phdr: 9a23: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
Ironport-sdr: H29RHkRz9/4PuvA5IQmUDhckFC68oZEXvSzc/PZ6Szo6Dke3W+hVgdxeK2Km/eBOgeaJO7pccE d+Y3eYWYe8l3ULQLKEwzJf6mURmuAZ3lNXFyr86A/E8dwdzFplLMHOfseVvsamA3GrEqJeIkGq QV8fLVpkhHXJBc+W7c+6tHwv/IE2860VbSSEIqIHn/eiBghTkFBNSaMdBQrUuvP/Aar58b2hqC DvyjXO2oR3Yt+rtNUagBGpd1mndQ0AVXyx0i+adXtC2twQ2UTbtFV9ovy+yjDrLqfvO9j/kZrN SN0=
Organization: Institut für Kernphysik Mainz

Hello again,

I realized, that with my rather slow home office internet connection opening the seafile-links takes forever (it'll display all 79000 lines of the file).

You can use this direct download link if you want:

https://seafile.rlp.net/f/f810b1f514da4a6bb446/?dl=1

Best regards

Simon

Am 05.10.2020 um 12:08 schrieb Dr. Simon Friederich:

Dear OPAL-Team,

I wanted to simulate using
mpirun -np 2 opal input.in

The simulation "opal input.in" runs perfectly fine without errors, but using mpirun shows multiple error messages over and over again and the results look 'strangely merged'(?; don't know how to call it; I've put two pictures in the attachement).

Here are some main error messages (the step number changes)

    [proc 0] E: H5WriteStepAttribString: Cannot overwrite attribute /Step#0/OPAL_flavour
    Error> H5 rc= -2 in /home/frieders/opal/opal_source/git-OPAL-src/src/Structure/H5PartWrapperForPT.cpp @ line 326
    [proc 0] E: H5WriteStepAttribFloat64: Cannot overwrite attribute /Step#0/SPOS
    ...

[proc 0] E: H5SetStep: Cannot query link //Step#346.
...

[proc 0] E: H5WriteStepAttribFloat64: Iteration is invalid! Have you set the time step?
Error> H5 rc= -2 in /home/frieders/opal/opal_source/git-OPAL-src/src/Structure/H5PartWrapperForPT.cpp @ line 375

I've saved the complete terminal output here:
https://seafile.rlp.net/f/f810b1f514da4a6bb446/

I guess the error occurs because I've done something wrong when compiling OPAL
(either within needed toolchain or within the making of OPAL; I have used the "OPAL-2.4" branch with commit ffded40c6dd317d).

I guess it has something to do with h5hut. Do you have any hint for me, where to look for? Can I test h5hut by itself?

(Until now I've only used a virtual machine using Debian 10, but now I've a desktop-pc with Ubuntu 20.04.1 LTS at hand, where the error occurs too.)

Best regards and thank you very much in advance

Simon

-- 
Dr. Simon Friederich
Helmholtz-Institut Mainz
Kollaboration B/ACID
Johannes Gutenberg-Universität Mainz
Staudingerweg 18
55128 Mainz, Deutschland

Tel.: +49 (0)6131 39-23160
E-Mail: s.friederich AT uni-mainz.de

-- 
Dr. Simon Friederich
Helmholtz-Institut Mainz
Kollaboration B/ACID
Johannes Gutenberg-Universität Mainz
Staudingerweg 18
55128 Mainz, Deutschland

Tel.: +49 (0)6131 39-23160
E-Mail: s.friederich AT uni-mainz.de

[Opal] mpirun H5WriteStepAttribFloat64, Dr. Simon Friederich, 10/05/2020
- Re: [Opal] mpirun H5WriteStepAttribFloat64, Dr. Simon Friederich, 10/05/2020
- Re: [Opal] mpirun H5WriteStepAttribFloat64, Gsell Achim (PSI), 10/05/2020