Trac April 2016

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107 discussions

[Einstein Toolkit] #1743: Reduce number of output files per directory
by Einstein Toolkit 16 Jan '17

16 Jan '17

#1743: Reduce number of output files per directory ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: unset | Milestone: Component: Other | Version: development version Keywords: | ----------------------+----------------------------------------------------- Reduce the number of output files per directory in CarpetIOHDF5 by creating a hierarchy of subdirectories. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1743> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1819: CarpetMask: add option to exclude boxes
by Einstein Toolkit 16 Jan '17

16 Jan '17

#1819: CarpetMask: add option to exclude boxes -------------------------------------+-------------------------------------- Reporter: bmundim | Owner: eschnett Type: enhancement | Status: new Priority: unset | Milestone: Component: Carpet | Version: development version Keywords: CarpetMask CarpetReduce | -------------------------------------+-------------------------------------- I would like to be able to exclude boxes in addition to spherical surfaces when setting the CarpetMask::weight (which is used by CarpetReduce to exclude regions when performing reductions). The following pull request implements this functionality: {{{ https://bitbucket.org/eschnett/carpet/pull-requests/5/bcm-carpetmask/diff }}} I have some parameter files I used to test my implementation. I can turn them into testsuites after the revision of this ticket. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1819> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1861: NaNChecker: do not report missing storage when checking "all" variables
by Einstein Toolkit 01 Jan '17

01 Jan '17

#1861: NaNChecker: do not report missing storage when checking "all" variables -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: Formaline | -----------------------------------+---------------------------------------- pull request at https://bitbucket.org/cactuscode/cactusutils/pull- requests/6/nanchecker-do-not-report-missing-storage/diff removes lots of output about variables having no storage if checking all variables for NaN is requested. Since "all" variables means "all that could be defined" and not "all that are turned on" there is always lots of clutter when "all" is used. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1861> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #394: Testsuite log file should contain more information
by Einstein Toolkit 12 Dec '16

12 Dec '16

#394: Testsuite log file should contain more information -------------------------+-------------------------------------------------- Reporter: hinder | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: testsuites | -------------------------+-------------------------------------------------- It is useful to look at the testsuite log file for information about how the tests were run. For example, which compiler was used, and with what compiler options. We need to balance this against providing information which will always change, making diffs hard to read. The most extreme case would be to output all make variables. Maybe better would be to output CC, CFLAGS, CXX, etc. Another option would be to parse these and say "intel compiler", "gcc", "pgi" etc. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/394> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1717: hwloc: lnuma & lltdl *really* required?
by Einstein Toolkit 06 Dec '16

06 Dec '16

#1717: hwloc: lnuma & lltdl *really* required? -----------------------------------+---------------------------------------- Reporter: zachetie@… | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: | -----------------------------------+---------------------------------------- I downloaded the ET devel version (ca. Nov 26) on my (ubuntu) laptop and compiled it, using gcc. I compiled to the linker stage, and the linker complained: ld: cannot find -lnuma ld: cannot find -lltdl I found references to these libraries in: configs/[buildname]/bindings/Configuration/Capabilities/make.HWLOC.defn After removing these references, the code compiled and seemed (on the surface) to run okay. Are these libraries really necessary? I ask because every time I need to install ET on a new machine, it would be more convenient if the step "apt-get install libnuma-dev libltdl-dev" were left out, particularly since reliable Internet access may not exist at that time. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1717> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1835: simfactory website contains incorrect download location
by Einstein Toolkit 06 Dec '16

06 Dec '16

#1835: simfactory website contains incorrect download location ------------------------+--------------------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: major | Milestone: Component: SimFactory | Version: development version Keywords: | ------------------------+--------------------------------------------------- The simfactory website at http://simfactory.org/simfactory/download/ contains incorrect download instructions for simfactory2 since it still refers to the svn repository instead of the bitbucket one. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1835> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1656: CarpetInterp and MoL do not work properly together
by Einstein Toolkit 02 Nov '16

02 Nov '16

#1656: CarpetInterp and MoL do not work properly together --------------------+------------------------------------------------------- Reporter: hinder | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: Carpet | Version: development version Keywords: | --------------------+------------------------------------------------------- I am trying to integrate interpolated quantities using MoL. I call the interpolator in MoL_CalcRHS, and want it to perform only a spatial interpolation of the current content of timelevel 0. This current content is what has been set by MoL; it is not the final value that will be at t_{n+1} or was at t_N, but is the intermediate value that should be used when computing the RHS at a given MoL substep. Since MoL does not set the Carpet time hierarchy values, CarpetInterp seems to get confused about how to do the interpolation. I need to tell CarpetInterp not to interpolate in time at all, but to use timelevel 0 only. Unfortunately, setting the interpolator option to use only one timelevel does not work. There is commented-out code to "use cctk_time to decide whether to interpolate", which essentially guarantees that no time interpolation will happen (since the interpolation is requested for cctk_time, and the current time is cctk_time, so they are always equal). Re-enabling this code allowed me to achieve 4th order convergence for integrated interpolated quantities, though I am not sure I understand everything that is going on in CarpetInterp. I have added a parameter which controls this, and with this parameter set to the default, nothing changes (i.e. it is not going to change anyone's results unless they set the parameter). I would like to commit this, so that collaborators can work off the same version. Since the patch is very small, I hope this will not add too much unneeded complexity. Is it OK to commit? Patch is attached. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1656> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1622: Cannot log in to Blue Waters
by Einstein Toolkit 06 Oct '16

06 Oct '16

#1622: Cannot log in to Blue Waters ------------------------+--------------------------------------------------- Reporter: eschnett | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: SimFactory | Version: development version Keywords: | ------------------------+--------------------------------------------------- With the new gsissh mechanism in Simfactory, I receive the error below when I try to log in. {{{ $ ./bin/sim --verbose login bluewaters Info: Simfactory command: ./bin/../simfactory/lib/sim.py "--verbose" "login" "bluewaters" Info: Version 2356M Info: The Simulation Factory: Manage Cactus simulations Info: defs: /Users/eschnett/Cvanilla/simfactory/etc/defs.ini Info: defs.local: /Users/eschnett/Cvanilla/simfactory/etc/defs.local.ini Info: Executing command: login Info: Logging into remote machine bluewaters Info: executing command: /bin/bash -c '{ :; } && { { mkdir -p /Users/eschnett/Cvanilla/.globus && : >> /Users/eschnett/Cvanilla/.globus/proxy-tfca-ncsa && chmod go-rwx /Users/eschnett/Cvanilla/.globus/proxy-tfca-ncsa && export X509_USER_PROXY=/Users/eschnett/Cvanilla/.globus/proxy-tfca-ncsa && : mkdir -p /Users/eschnett/Cvanilla/.globus/certificates-tfca-ncsa && : export X509_CERT_DIR=/Users/eschnett/Cvanilla/.globus/certificates-tfca- ncsa && { { grid-proxy-info -issuer -file /Users/eschnett/Cvanilla/.globus/proxy-tfca- ncsa 2>/dev/null | grep "^/C=US/O=National Center for Supercomputing Applications/" >/dev/null 2>&1 && test $(grid-proxy-info -timeleft -file /Users/eschnett/Cvanilla/.globus /proxy-tfca-ncsa 2>/dev/null) -gt 0 2>/dev/null } || { { grid-proxy-destroy 2>/dev/null || true; } && myproxy-logon -p 7512 -s tfca.ncsa.illinois.edu -T -l eschnett -o /Users/eschnett/Cvanilla/.globus/proxy-tfca-ncsa } } && { globus-update-certificate-dir >/dev/null 2>&1 || true; }; } && gsissh -o UserKnownHostsFile=/Users/eschnett/Cvanilla/simfactory/etc/ssh_known_hosts -t eschnett(a)h2ologin.ncsa.illinois.edu '\''cd /u/sciteam/eschnett/Cvanilla || echo "Could not change to directory /u/sciteam/eschnett/Cvanilla"; $SHELL -l'\''; }' Enter MyProxy pass phrase: Failed to receive credentials. Failed writing buffer to BIO Failed unpacking proxy certificate from buffer Error accepting delegated credentials: Failed writing buffer to BIO Failed unpacking proxy certificate from buffer Error while executing command "/bin/bash -c '{ :; } && { { mkdir -p /Users/eschnett/Cvanilla/.globus && : >> /Users/eschnett/Cvanilla/.globus/proxy-tfca-ncsa && chmod go-rwx /Users/eschnett/Cvanilla/.globus/proxy-tfca-ncsa && export X509_USER_PROXY=/Users/eschnett/Cvanilla/.globus/proxy-tfca-ncsa && : mkdir -p /Users/eschnett/Cvanilla/.globus/certificates-tfca-ncsa && : export X509_CERT_DIR=/Users/eschnett/Cvanilla/.globus/certificates-tfca- ncsa && { { grid-proxy-info -issuer -file /Users/eschnett/Cvanilla/.globus/proxy-tfca- ncsa 2>/dev/null | grep "^/C=US/O=National Center for Supercomputing Applications/" >/dev/null 2>&1 && test $(grid-proxy-info -timeleft -file /Users/eschnett/Cvanilla/.globus /proxy-tfca-ncsa 2>/dev/null) -gt 0 2>/dev/null } || { { grid-proxy-destroy 2>/dev/null || true; } && myproxy-logon -p 7512 -s tfca.ncsa.illinois.edu -T -l eschnett -o /Users/eschnett/Cvanilla/.globus/proxy-tfca-ncsa } } && { globus-update-certificate-dir >/dev/null 2>&1 || true; }; } && gsissh -o UserKnownHostsFile=/Users/eschnett/Cvanilla/simfactory/etc/ssh_known_hosts -t eschnett(a)h2ologin.ncsa.illinois.edu '\''cd /u/sciteam/eschnett/Cvanilla || echo "Could not change to directory /u/sciteam/eschnett/Cvanilla"; $SHELL -l'\''; }'": Command returned exit status 1 eschnett@Redshift:~/Cvanilla (16:40:03) $ ./bin/sim login bluewaters Enter MyProxy pass phrase: Failed to receive credentials. Failed writing buffer to BIO Failed unpacking proxy certificate from buffer Error accepting delegated credentials: Failed writing buffer to BIO Failed unpacking proxy certificate from buffer }}} -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1622> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1865: Automatically start SystemTopology
by Einstein Toolkit 03 Oct '16

03 Oct '16

#1865: Automatically start SystemTopology ---------------------------------+------------------------------------------ Reporter: dradice@… | Owner: eschnett Type: enhancement | Status: new Priority: major | Milestone: Component: Carpet | Version: development version Keywords: | ---------------------------------+------------------------------------------ Carpet used to load hwloc automatically and that would set thread affinities. Now this functionality is in the SystemTopology thorn, which is not automatically activated. This change could result in a significant performance regression on some systems (see discussion in #1850). Would it make sense to activate SystemTopology automatically? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1865> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1873: Parameter file parser cannot handle empty files
by Einstein Toolkit 25 Sep '16

25 Sep '16

#1873: Parameter file parser cannot handle empty files ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: | ----------------------+----------------------------------------------------- I used a parameter file that was empty except for comments: {{{ # ActiveThorns = "PUGH" # ActiveThorns = "MultiThreading" # ActiveThorns = "FunHPC" }}} Cactus complais about this: {{{ Activating thorn Cactus...Success -> active implementation Cactus WARNING level 0 from host process 0 while executing schedule bin (none), routine (no thorn)::(no routine) in thorn cactus, file multithreading.par:1: -> ERROR IN PARAMETER FILE:In rule 'file::skipper' Line=3, Column=84 # ActiveThorns = "PUGH" # ActiveThorns = "MultiThreading" # ActiveThorns = "FunHPC" }}} -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1873> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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