Trac September 2015

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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] #1816: segfaults on 64bit systems when build with c99
by Einstein Toolkit 17 Aug '16

17 Aug '16

#1816: segfaults on 64bit systems when build with c99 --------------------------------+------------------------------------------- Reporter: physik@… | Owner: Type: defect | Status: new Priority: unset | Milestone: Component: Cactus | Version: ET_2014_05 Keywords: | --------------------------------+------------------------------------------- I recently encountered a segfault in ScheduleInterface.c, more precisely in the function static int CCTKi_ScheduleCallFunction(void *function, t_attribute *attribute, t_sched_data *data) { /* find the timer for this function and this schedule bin */ t_timer *timer = attribute->timers; while (timer && strcmp(timer->schedule_bin, data->schedule_bin)) { timer = timer->next; } Running in the debugger revealed that timer->schedule_bin pointed to an invalid address. Curiously, it had the top 33 (33 not a typo) bits all set. Taking the lowest 32 bits gave a valid address which pointed to a reasonable string "CCTK_INITIAL". This suggests a 32/64 bit issue. The pointer timer->schedule_bin seems to be initialized in the same function using strdup: timer->schedule_bin = strdup (where); strdup is not part of the c99 standard, but only Posix. Compiling with gcc --std=c99 means it is not defined in <string.h>. This means the compiler treats the occurrence of strdup as an implicit function declaration, and assumes it returns int. Thus, it will do an implicit conversion of the result from int to char*. If the highest bit of the int was set, this resulted in a 64 bit pointer with all 32 high bits set (I checked with a small test code). When the address returned by the actual strdup code linked from glibc has the top 33 bits zero, the conversion yields the correct results. Therefore, the problem is hard to reproduce, it only occurred with a test case almost exhausting my workstations memory, but frustratingly not small tests. After this, I also found compiler warnings for ScheduleInterface.c of the type implicit declaration of function ‘strdup’ [-Wimplicit-function- declaration] and assignment makes pointer from integer without a cast [-Wint-conversion] Switching from --std=c99 to --std=gnu99 fixed the problem for now. However, this is a bug that might affect many users since the code compiles with --std=c99 and the compiler warnings are hidden within the thousands of other compiler warnings the ET code generates. Also, a quick grep revealed many occurrences of strdup, although some of them where redefined as Util_Strdup. The rest might lead to segfaults on 64 bit systems with std=c99. My findings concern the Wheeler release, I haven't had time to check the development version. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1816> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1791: Allow aligning the interior of grid functions in looping macros
by Einstein Toolkit 28 Jun '16

28 Jun '16

#1791: Allow aligning the interior of grid functions in looping macros -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: | -------------------------+-------------------------------------------------- Currently, when grid functions are aligned, Cactus expects their origin to be aligned. These changes update the looping macros to allow aligning the interior of grid functions instead. Whether and how grid functions are aligned is still determined by the driver -- this only makes it possible to still use the looping macros in this case. Implemented in <https://bitbucket.org/cactuscode/cactus/pull-request/16 /allow-aligning-the-interior-of-grid/diff> and <https://bitbucket.org/cactuscode/cactustest/pull-request/1/allow- aligning-the-interior-of-grid/diff>. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1791> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1657: ExternalThorns/pciutils ignores most option list options
by Einstein Toolkit 28 Jun '16

28 Jun '16

#1657: ExternalThorns/pciutils ignores most option list options -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: pciutils | -----------------------------------+---------------------------------------- It does not contain a configure script and its Makefile hard-codes the compiler and linker to be gcc. This is an issue if LDFLAGS (or CFLAGS possibly) contain {{{-openmp}}} like they do when using the intel compiler. Also using mkl could (should) be done with the {{{-mkl}}} switch to the intel compiler but gcc (as used in pciutils) will naturally not accept this. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1657> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1697: testing system starts tests for which thorns are missing
by Einstein Toolkit 27 Jun '16

27 Jun '16

#1697: testing system starts tests for which thorns are missing --------------------+------------------------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: | --------------------+------------------------------------------------------- We apparently have a bug in the perl script that drives the testsuite. On hydra (a machine at RZG that Ian and I are testing) it tries to run the test_ah test of Dissipation even though that test parfile uses NoExcision which is commented out. A quick test indicates that the script only looks at the first ActiveThorns line in the parfile when it determines if a parfile is runnable. Movin NoExcision into the first ActiveThorns line correctly ignores the test on hydra. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1697> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1623: using ENV in parfiles is not documented
by Einstein Toolkit 25 Jun '16

25 Jun '16

#1623: using ENV in parfiles is not documented ---------------------------+------------------------------------------------ Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: documentation | ---------------------------+------------------------------------------------ the user guide does not explain how to use ENV in parfiles (at least grep ENV doc/UsersGuide/*.tex does not find anything) nor do the peg files in src/piraha/peg contain. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1623> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1759: need tensorparity=-1 for WeylScal4::curvIi_group and curvJi_group
by Einstein Toolkit 13 Jun '16

13 Jun '16

#1759: need tensorparity=-1 for WeylScal4::curvIi_group and curvJi_group ------------------------------------+--------------------------------------- Reporter: physicsbeany@… | Owner: Bernard Kelly Type: defect | Status: new Priority: minor | Milestone: ET_2014_11 Component: EinsteinToolkit thorn | Version: development version Keywords: weylscal4, parity | ------------------------------------+--------------------------------------- The WeylScal4 gridfunctions curvIi and curvJi are pesudoscalars with the same parity properties as Psi2r and Psi2i. However, they're currently assigned no tensorparity attribute, so they're treated as scalars. As a result, for a z-aligned Kerr BH (EinsteinInitialData/IDAnalyticBH) evolved with reflection symmetry across the x-y plane, an interpolation of curvIi to a coordinate sphere will yield different values for the z<0 points than the same data on a full grid. Can we set "tensorparity=-1" for both these groups, to fix this issue? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1759> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #382: SimFactory home directory on Kraken is too specific
by Einstein Toolkit 01 Jun '16

01 Jun '16

#382: SimFactory home directory on Kraken is too specific ------------------------+--------------------------------------------------- Reporter: hinder | Owner: mthomas Type: defect | Status: new Priority: major | Milestone: ET_2011_05 Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- The mdb entry for Kraken in SimFactory has 'sourcebasedir' => '/nics/b/home/@USER@', My home directory is '/nics/d/home/@USER@' Either we could leave the source base dir as unset to force the user to set it, or we could automatically detect the location of the user's home directory (better). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/382> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #960: Dissipation thorn schedules LOCAL routines after GLOBAL ones
by Einstein Toolkit 27 May '16

27 May '16

#960: Dissipation thorn schedules LOCAL routines after GLOBAL ones ----------------------------------------------+----------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: Dissipation and SphericalSurface | ----------------------------------------------+----------------------------- Dissipation currently contains a schedule item {{{ SCHEDULE setup_epsdis AT cctk_poststep after SphericalSurface_HasBeenSet { LANG: C SYNC: epsdisA_group } "Setup spatially varying dissipation" }}} However SphericalSurface_HasBeenSet is AFTER SphericalSurface_Set which is a GLOBAL routine. Since GLOBAL routines run last in POSTSTEP (which is in EVOL) the AFTER modifier is ignored for all but the last (finest) refinement level. This can lead to the wrong surface shape to be used by the local routines. It might actually make sense to teach the flesh about GLOBAL/LOCAL etc and refuse AFTER/BEFORE statements that span different modes. This of course depends on how much work this is and if we expect the dependency and task based scheduler to be finished soon and if there are legitimate uses for AFTER/BEFORE to span modes. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/960> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #912: Use CACTUS_CONFIGS_DIR in Formaline
by Einstein Toolkit 23 May '16

23 May '16

#912: Use CACTUS_CONFIGS_DIR in Formaline -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- Formaline assumes that configurations are stored in a "configs" subdirectory of $CCTK_HOME. Use $CACTUS_CONFIGS_DIR instead. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/912> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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