Users October 2015

users@lists.einsteintoolkit.org

14 participants
25 discussions

Ideas for a new I/O file format
by Erik Schnetter 06 Oct '15

06 Oct '15

This Monday we briefly discussed various concepts related to a new I/O file format for Cactus, and I presented a graphical overview of these concepts. I have now written things up in a C++-like style and added it to the wiki < https://docs.einsteintoolkit.org/et-docs/A_new_I/O_file_format>. -erik -- Erik Schnetter <eschnetter(a)perimeterinstitute.ca> http://www.perimeterinstitute.ca/personal/eschnetter/ AIM: eschnett247, Skype: eschnett, Google Talk: schnetter(a)gmail.com

1 0

Simulation olog
by Erik Schnetter 05 Oct '15

05 Oct '15

[image: Inline image 1] -- Erik Schnetter <schnetter(a)gmail.com> http://www.perimeterinstitute.ca/personal/eschnetter/

1 0

Re: [Users] HDF5 Error, Hilbert
by Geraint Pratten 05 Oct '15

05 Oct '15

Hi, I am trying to run a simulation with the same output directory - though I've been removing the simulations after each run while trying to fix the above issue. I should have write access to the file and there should be sufficient storage. Geraint On 5 October 2015 at 11:34, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: > > On 1 Oct 2015, at 15:49, Erik Schnetter <schnetter(a)cct.lsu.edu> wrote: > > Geraint > > Some very fundamental HDF5 operations fail. This could be due to a file > system problem; maybe you don't have write access to the file, or your disk > is full. It could also be that there exists a corrupted HDF5 file, and you > are trying to write to it (extend it). > > HDF5 files can get corrupted if you have opened it for writing, and then > the application is interrupted or crashes, or you run out of disk space. > Even if you make free space later, a corrupted file remains corrupted. > > > Hi Geraint, > > Are you trying to run a simulation with output in the same directory as > one that was run before? > > > -erik > > > On Thu, Oct 1, 2015 at 9:30 AM, Geraint Pratten <g.pratten(a)sussex.ac.uk> > wrote: > >> Hi all, >> >> I recently built the latest release (Hilbert) on the local cluster and >> I've been getting a HDF5 error. I've tried building Cactus with both the >> local HDF5 package on the cluster as well as letting Cactus build HDF5 from >> scratch. Does anyone have any insight into the error I've attached below >> (extract of a long chain of errors of the same form)? >> >> I can dump the output to file or give configuration files if needed. >> >> Thanks in advance! >> Geraint >> >> ---------- >> >> HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0: >> #000: H5Ddeprec.c line 193 in H5Dcreate1(): unable to create dataset >> major: Dataset >> minor: Unable to initialize object >> #001: H5Dint.c line 453 in H5D__create_named(): unable to create and >> link to dataset >> major: Dataset >> minor: Unable to initialize object >> #002: H5L.c line 1638 in H5L_link_object(): unable to create new link >> to object >> major: Links >> minor: Unable to initialize object >> #003: H5L.c line 1882 in H5L_create_real(): can't insert link >> major: Symbol table >> minor: Unable to insert object >> #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal >> failed >> major: Symbol table >> minor: Object not found >> #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator >> failed >> major: Symbol table >> minor: Callback failed >> #006: H5L.c line 1674 in H5L_link_cb(): name already exists >> major: Symbol table >> minor: Object already exists >> WARNING level 1 from host node207.cm.cluster process 0 >> while executing schedule bin (none), routine (no thorn)::(no routine) >> in thorn CarpetIOHDF5, file >> /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc >> :677: >> -> HDF5 call 'dataset = H5Dcreate (outfile, datasetname.str().c_str(), >> filedatatype, dataspace, plist)' returned error code -1 >> WARNING level 1 from host node207.cm.cluster process 0 >> while executing schedule bin (none), routine (no thorn)::(no routine) >> in thorn CarpetIOHDF5, file >> /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc >> :689: >> -> HDF5 call 'H5Dwrite (dataset, memdatatype, H5S_ALL, H5S_ALL, >> H5P_DEFAULT, data)' returned error code -1 >> WARNING level 1 from host node207.cm.cluster process 0 >> while executing schedule bin (none), routine (no thorn)::(no routine) >> in thorn CarpetIOHDF5, file >> /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc >> :725: >> -> HDF5 call 'attr = H5Acreate (dataset, "level", H5T_NATIVE_INT, >> dataspace, H5P_DEFAULT)' returned error code -1 >> WARNING level 1 from host node207.cm.cluster process 0 >> while executing schedule bin (none), routine (no thorn)::(no routine) >> in thorn CarpetIOHDF5, file >> /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc >> :726: >> -> HDF5 call 'H5Awrite (attr, H5T_NATIVE_INT, &refinementlevel)' >> returned error code -1 >> WARNING level 1 from host node207.cm.cluster process 0 >> >> -- >> Geraint Pratten >> Postdoctoral Research Associate >> >> Mobile: +44(0) 7581709282 >> E-mail: G.Pratten(a)sussex.ac.uk >> Skype: geraint.pratten >> >> School of Mathematical and Physical Sciences >> Pevensey 3 Building >> University of Sussex >> Falmer Campus >> Brighton >> BN1 9QH >> United Kingdom >> >> _______________________________________________ >> Users mailing list >> Users(a)einsteintoolkit.org >> http://lists.einsteintoolkit.org/mailman/listinfo/users >> >> > > > -- > Erik Schnetter <schnetter(a)cct.lsu.edu> > http://www.perimeterinstitute.ca/personal/eschnetter/ > _______________________________________________ > Users mailing list > Users(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users > > > -- > Ian Hinder > http://members.aei.mpg.de/ianhin > > -- Geraint Pratten Postdoctoral Research Associate Mobile: +44(0) 7581709282 E-mail: G.Pratten(a)sussex.ac.uk Skype: geraint.pratten School of Mathematical and Physical Sciences Pevensey 3 Building University of Sussex Falmer Campus Brighton BN1 9QH United Kingdom

2 1

HDF5 Error, Hilbert
by Geraint Pratten 05 Oct '15

05 Oct '15

Hi all, I recently built the latest release (Hilbert) on the local cluster and I've been getting a HDF5 error. I've tried building Cactus with both the local HDF5 package on the cluster as well as letting Cactus build HDF5 from scratch. Does anyone have any insight into the error I've attached below (extract of a long chain of errors of the same form)? I can dump the output to file or give configuration files if needed. Thanks in advance! Geraint ---------- HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0: #000: H5Ddeprec.c line 193 in H5Dcreate1(): unable to create dataset major: Dataset minor: Unable to initialize object #001: H5Dint.c line 453 in H5D__create_named(): unable to create and link to dataset major: Dataset minor: Unable to initialize object #002: H5L.c line 1638 in H5L_link_object(): unable to create new link to object major: Links minor: Unable to initialize object #003: H5L.c line 1882 in H5L_create_real(): can't insert link major: Symbol table minor: Unable to insert object #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed major: Symbol table minor: Object not found #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed major: Symbol table minor: Callback failed #006: H5L.c line 1674 in H5L_link_cb(): name already exists major: Symbol table minor: Object already exists WARNING level 1 from host node207.cm.cluster process 0 while executing schedule bin (none), routine (no thorn)::(no routine) in thorn CarpetIOHDF5, file /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc:677: -> HDF5 call 'dataset = H5Dcreate (outfile, datasetname.str().c_str(), filedatatype, dataspace, plist)' returned error code -1 WARNING level 1 from host node207.cm.cluster process 0 while executing schedule bin (none), routine (no thorn)::(no routine) in thorn CarpetIOHDF5, file /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc:689: -> HDF5 call 'H5Dwrite (dataset, memdatatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, data)' returned error code -1 WARNING level 1 from host node207.cm.cluster process 0 while executing schedule bin (none), routine (no thorn)::(no routine) in thorn CarpetIOHDF5, file /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc:725: -> HDF5 call 'attr = H5Acreate (dataset, "level", H5T_NATIVE_INT, dataspace, H5P_DEFAULT)' returned error code -1 WARNING level 1 from host node207.cm.cluster process 0 while executing schedule bin (none), routine (no thorn)::(no routine) in thorn CarpetIOHDF5, file /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc:726: -> HDF5 call 'H5Awrite (attr, H5T_NATIVE_INT, &refinementlevel)' returned error code -1 WARNING level 1 from host node207.cm.cluster process 0 -- Geraint Pratten Postdoctoral Research Associate Mobile: +44(0) 7581709282 E-mail: G.Pratten(a)sussex.ac.uk Skype: geraint.pratten School of Mathematical and Physical Sciences Pevensey 3 Building University of Sussex Falmer Campus Brighton BN1 9QH United Kingdom

3 2

disabling subcycling
by Steven R. Brandt 03 Oct '15

03 Oct '15

I want to disable subcycling in time. To do this, I followed Erik's advice and set Carpet::time_refinement_factors = "[1,1,1]" However, I still get this error message: ERROR from host sbrandt-think.cct.lsu.edu process 0 while executing schedule bin (none), routine (no thorn)::(no routine) in thorn CarpetLib, file /home/sbrandt/cactus/CactusFW2/arrangements/Carpet/CarpetLib/src/ggf.cc:379: -> The variable "FUNWAVE::mask" has only 1 active time levels, which is not enough for boundary prolongation of order 1 cactus_sim: /home/sbrandt/cactus/CactusFW2/arrangements/Carpet/Carpet/src/helpers.cc:324: int Carpet::Abort(const cGH*, int): Assertion `0' failed. If my time refinement is 1, then 1 time level should be adequate. Right? Cheers, Steve

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

Users October 2015