Trac July 2011

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[Einstein Toolkit] #419: CarpetRegrid2 sets up grids which are not consistent
by Einstein Toolkit 06 Jul '11

06 Jul '11

#419: CarpetRegrid2 sets up grids which are not consistent --------------------+------------------------------------------------------- Reporter: knarf | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: | --------------------+------------------------------------------------------- The attached parfile creates a grid using CarpetRegrid2 (hg version), which CarpetReduce later warns about: INFO (CarpetReduce): Simulation domain volume: 4096 INFO (CarpetReduce): Reduction weight sum: 4468.125 WARNING[L1,P0] (CarpetReduce): Simulation domain volume and reduction weight sum differ The grid info is: INFO (Carpet): Grid structure (superregions, grid points): [0][0][0] exterior: [0,0,0] : [21,21,21] ([22,22,22] + PADDING) 10648 [1][0][0] exterior: [3,3,3] : [40,40,40] ([38,38,38] + PADDING) 54872 [2][0][0] exterior: [9,9,9] : [42,42,42] ([34,34,34] + PADDING) 39304 [3][0][0] exterior: [21,21,21] : [52,52,52] ([32,32,32] + PADDING) 32768 [4][0][0] exterior: [45,45,45] : [72,72,72] ([28,28,28] + PADDING) 21952 INFO (Carpet): Grid structure (superregions, coordinates): [0][0][0] exterior: [-48,-48,-48] : [288,288,288] : [16,16,16] [1][0][0] exterior: [-24,-24,-24] : [272,272,272] : [8,8,8] [2][0][0] exterior: [-12,-12,-12] : [120,120,120] : [4,4,4] [3][0][0] exterior: [-6,-6,-6] : [56,56,56] : [2,2,2] [4][0][0] exterior: [-3,-3,-3] : [24,24,24] : [1,1,1] -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/419> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #469: Improve default directory locations
by Einstein Toolkit 06 Jul '11

06 Jul '11

#469: Improve default directory locations -------------------------+-------------------------------------------------- Reporter: hinder | Owner: eschnett Type: enhancement | Status: new Priority: minor | Milestone: Component: SimFactory | Version: Keywords: | -------------------------+-------------------------------------------------- It is usually desirable to set the user's source base directory to be in their home directory. On many systems, this can be inferred from the user name; e.g. /home/@USER@. However, on systems with very large numbers of users, the home directory is sometimes not predictable in this way. For example, /home1/00915/@USER@ (this is on LoneStar), where the numbers are different for different users. This also happens on Kraken (see ticket #382). Having to specify these details manually for each machine that you want to use is an extra step in configuring SimFactory which we would like to avoid. Option 1: Provide a @HOME@ definition which is determined automatically from the user's home directory. This would be possible, but it only solves the problem for the home directory. On some systems (again, LoneStar and Kraken), the home directory might not be large enough to use as a source base directory, and instead you might want to use the "work" directory instead (this is the current simfactory setting for LoneStar). This directory also suffers from the same unpredictable numbering problems. As the home directory is available in the HOME environment variable, the work directory is available in the WORK environment variable. Option 2: Provide a general method for accessing environment variables and storing them in definitions. For example, you could write @ENV(HOME)@ or @ENV(WORK)@. This requires the environment to have been correctly set up (for remote operation, this requires a login shell, but I think we have that already). In fact it looks like there is preliminary code in simsubs.py, but it is incomplete and is not called from anywhere. I would favour option 2. Thoughts? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/469> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #381: Cannot log in to Kraken using default simfactory configuration
by Einstein Toolkit 06 Jul '11

06 Jul '11

#381: Cannot log in to Kraken using default simfactory configuration ------------------------+--------------------------------------------------- Reporter: hinder | Owner: mthomas Type: defect | Status: new Priority: major | Milestone: ET_2011_05 Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- SimFactory uses the gsissh method to connect to Kraken. This requires a "proxy" to be created locally via the myproxy-logon command. There is currently logic in Perl simfactory's mdb.pm file to automatically run myproxy-logon and prompt for the passphrase. This does not work for me. I get the error Failed to receive credentials. ERROR from myproxy-server (myproxy.teragrid.org): PAM authentication failed: Permission denied (see below for the full output). If I remove the localsshsetup key, I can run the myproxy-logon command manually and then connect using simfactory. Looking at the full output below, it seems that it is trying to run myproxy-logon with my local username (ian) instead of the remote one (hinder). If I replace the @USER@ in the myproxy-logon command with my Kraken username, everything works as expected. MacBook:etrelease ian$ sim login kraken Simulation Factory: Executing: { mkdir -p /Users/ian/Cactus/etrelease/.globus && : >> /Users/ian/Cactus/etrelease/.globus/proxy-teragrid && chmod go-rwx /Users/ian/Cactus/etrelease/.globus/proxy-teragrid && export X509_USER_PROXY=/Users/ian/Cactus/etrelease/.globus/proxy-teragrid && : mkdir -p /Users/ian/Cactus/etrelease/.globus/certificates-teragrid && : export X509_CERT_DIR=/Users/ian/Cactus/etrelease/.globus/certificates- teragrid && { { grid-proxy-info -issuer -file /Users/ian/Cactus/etrelease/.globus /proxy-teragrid 2>/dev/null | grep "^/C=US/O=National Center for Supercomputing Applications/" >/dev/null 2>/dev/null && test $(grid-proxy-info -timeleft -file /Users/ian/Cactus/etrelease/.globus/proxy-teragrid 2>/dev/null) -gt 0 2>/dev/null } || { { grid-proxy-destroy 2>/dev/null || true; } && myproxy-logon -p 7514 -s myproxy.teragrid.org -T -l ian -o /Users/ian/Cactus/etrelease/.globus/proxy-teragrid } } && { globus-update-certificate-dir > /dev/null 2>&1 || true; }; } && gsissh -t hinder(a)kraken-gsi2.nics.teragrid.org '{ source /etc/profile; } && cd /nics/b/home/hinder/Cactus/etrelease && $SHELL -l' Enter MyProxy pass phrase: Failed to receive credentials. ERROR from myproxy-server (myproxy.teragrid.org): PAM authentication failed: Permission denied -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/381> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #113: Simfactory should be able to run the Cactus testsuites
by Einstein Toolkit 05 Jul '11

05 Jul '11

#113: Simfactory should be able to run the Cactus testsuites -------------------------+-------------------------------------------------- Reporter: knarf | Owner: mthomas Type: enhancement | Status: new Priority: critical | Milestone: ET_2011_06 Component: SimFactory | Version: Keywords: | -------------------------+-------------------------------------------------- ... in the python version, before the next ET release. The scripts at http://einsteintoolkit.org/release-info/ might help with implementing that. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/113> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #466: --reconfig seems to change thorn list
by Einstein Toolkit 04 Jul '11

04 Jul '11

#466: --reconfig seems to change thorn list ------------------------+--------------------------------------------------- Reporter: eschnett | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- The option --reconfig (without also giving a thorn list) seems to change the thorn list. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/466> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #464: create-submit without simulation name gives bad error message
by Einstein Toolkit 04 Jul '11

04 Jul '11

#464: create-submit without simulation name gives bad error message ------------------------+--------------------------------------------------- Reporter: eschnett | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- Calling create-submit without specifying a simulation name does not give a legible error message: $ ./bin/sim create-submit --debug Info: Simfactory command: ./bin/../simfactory/lib/sim.py "create-submit" " --debug" Info: Version 1371M The Simulation Factory: Manage Cactus simulations Info: defs: /Users/eschnett/EinsteinToolkit-hg- vanilla/simfactory/etc/defs.ini Info: defs.local: /Users/eschnett/EinsteinToolkit-hg- vanilla/simfactory/etc/defs.local.ini Info: Cactus Directory: /Users/eschnett/EinsteinToolkit-hg-vanilla Info: simenv.COMMAND: create-submit Info: Executing command: create_submit Traceback (most recent call last): File "./bin/../simfactory/lib/sim.py", line 147, in <module> main() File "./bin/../simfactory/lib/sim.py", line 143, in main CommandDispatch() File "./bin/../simfactory/lib/sim.py", line 105, in CommandDispatch module.main() File "/Users/eschnett/EinsteinToolkit-hg-vanilla/simfactory/lib/sim- manage.py", line 345, in main CommandDispatch() File "/Users/eschnett/EinsteinToolkit-hg-vanilla/simfactory/lib/sim- manage.py", line 324, in CommandDispatch exec("command_%s()" % command) File "<string>", line 1, in <module> File "/Users/eschnett/EinsteinToolkit-hg-vanilla/simfactory/lib/sim- manage.py", line 125, in command_create_submit simulationName = simenv.OptionsManager.args.pop(0) IndexError: pop from empty list -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/464> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #455: Sort link directories so that system directories come last
by Einstein Toolkit 03 Jul '11

03 Jul '11

#455: Sort link directories so that system directories come last ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | ----------------------+----------------------------------------------------- The enclosed patch ensures (makes it more likely) that external libraries provided by Cactus ("ExternalLibraries") supersede system libraries. The underlying problem is that all library search paths specified via -L are concatenated on the final link line, and if different versions of the same library exist, it is then difficult to ensure that that right one is used. The enclosed patch sorts the directories in final link line such that system directories (in particular /opt/local) come last, so that Cactus's directories come first. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/455> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #372: Accept comments in multi-line strings in parameter files
by Einstein Toolkit 02 Jul '11

02 Jul '11

#372: Accept comments in multi-line strings in parameter files -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- The attached patch modifies the parameter file parser to accept comments in multi-line strings. These comments extend from a "#" character to the end of the line. This makes it much easier to comment out variables in output strings. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/372> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #463: inlcude XXX_EARLY and XXX_LATE modes in schedule documentation, update "if" in schedule.ccl
by Einstein Toolkit 02 Jul '11

02 Jul '11

#463: inlcude XXX_EARLY and XXX_LATE modes in schedule documentation, update "if" in schedule.ccl -------------------+-------------------------------------------------------- Reporter: rhaas | Type: enhancement Status: new | Priority: optional Milestone: | Component: Cactus Version: | Keywords: documentation -------------------+-------------------------------------------------------- Two patches to the documentation. The first adds short one sentence descriptions of GLOBAL-EARLY, GLOBAL-LATE, META-EARLY and META-LATE. The second changes the documented allowed "if" statements in schedule files from {{{ if(CCTK_EQUALS(<parameter>, <value>)) { ... } }}} to {{{ if(<expression>) { ... } }}} which is what is actually allowed (and commonly used). Looking at the schedule parser it seems that in fact *everything* that is not a STORAGE/COMM or SCHEDULE block (or comment) is copied verbatim into the C function (tested this only very sporadically). Should this be documented? This affects the flesh so I cannot commit them myself. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/463> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #462: allow paramters in STORAGE statements
by Einstein Toolkit 02 Jul '11

02 Jul '11

#462: allow paramters in STORAGE statements -------------------------+-------------------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- the attached patch allows constructs such as: STORAGE metric[timelevels] instead of the currently used and more cumbersome: if(timelevels == 1) { STORAGE metric[1] } else if(timelevels == 2) { ... } The full set of Curie test suites pass (on my workstation usin gcc 4.6, OpenMP and 2 processes) with just that patch and with the second patch to GRHydro that actually uses the new facilities -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/462> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac July 2011