Trac November 2014

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159 discussions

[Einstein Toolkit] #1390: parameter file parser aborts when findeing first error
by Einstein Toolkit 19 May '17

19 May '17

#1390: parameter file parser aborts when findeing first error --------------------+------------------------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: development version Keywords: | --------------------+------------------------------------------------------- The attached parfile contains multiple errors (one per line). However the parameter file parser only reports the first one, then stops. This makes verifying parfiles for correctness hard. It might be good to defer aborting until the end of the file or until a larger number of parsing errors were encountered. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1390> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1172: Remove unnecessary exp/log calls in EOS_Omni
by Einstein Toolkit 18 May '17

18 May '17

#1172: Remove unnecessary exp/log calls in EOS_Omni -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- EOS_Omni seems to call exp/log more often than necessary in the nuc_eos table lookup routines. Use algebraic identities to remove them. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1172> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #614: relative tolerence in test.ccl of QuasiLocalMeasures very high
by Einstein Toolkit 12 Apr '17

12 Apr '17

#614: relative tolerence in test.ccl of QuasiLocalMeasures very high -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: optional | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- LSUThorns/QuasiLocalMeasures/test/test.ccl curerntly reads: {{{ ABSTOL 1.e-7 RELTOL 1.e+5 }}} I am curious: is the relative tolerance of 10,000 intentional or should it have been 1e-5 instead? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/614> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1276: Intel 2013.1.117 mis-compiles NewRad
by Einstein Toolkit 16 Mar '17

16 Mar '17

#1276: Intel 2013.1.117 mis-compiles NewRad -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: NewRad | -----------------------------------+---------------------------------------- Intels compiler fails (with -O2) to push values for bmin onto the stack in lines 316 of newrad.cc and line 126 of extrap.cc. Adding printf's for bmin perturbs the bug out of existence, but adding a printf of the address of bmax and reveals that at the time extrap_kernel is call the integer just before this address is still the initialization value of bmin[2] and not the correct value. The attached patch disables optimization for the two driver functions affected (but not the actual kernel). The patch is specific (via an #if) for this particular compiler and version. What is the best way of handling this? Target any intel version starting from the known failing one until we know of known good one? Or starting from an older known good one (that would be intel 11 in my case). Hopefully no similar bug is triggered by Carpet's use of the same idiom. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1276> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1439: SSL certificate check failing
by Einstein Toolkit 16 Mar '17

16 Mar '17

#1439: SSL certificate check failing --------------------+------------------------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Other | Version: development version Keywords: | --------------------+------------------------------------------------------- The check for SSL certificates in line 535: {{{#perl # check for svn SSL problems if ( $rec{"TYPE"} eq "svn" && defined $rec{"AUTH_URL"} ) { my $base = $rec{"AUTH_URL"}; $base =~ s/(https\:\/\/[\w\.]+)\/(.*)$/$1/i; unless ( defined $svn_servers{$base} ) { my $ret = `$svn --non-interactive info $rec{AUTH_URL} 2>&1`; if ( $ret =~ /Server certificate verification failed/ ) { $svn_servers{$base} = 0; } else { $svn_servers{$base} = 1; } } } }}} is incorrect since eg for the ET manifest where {{{ AUTH_URL=https://svn.einsteintoolkit.org/$1/trunk }}} the executed svn command is: {{{ svn --non-interactive info https://svn.einsteintoolkit.org/$1/trunk 2>&1 }}} which actually returns and error: {{{ svn: E175002: Unable to connect to a repository at URL 'https://svn.einsteintoolkit.org/trunk' svn: E175002: The OPTIONS request returned invalid XML in the response: XML parse error at line 1: Extra content at the end of the document (https://svn.einsteintoolkit.org/trunk) }}} but the code does not test for svn failures at all at this point. The simplest fix would be to move the check further down where {{{$1}}} has been replaced by an actual value, eg into the loop: {{{ # we are splitting each group of components into individuals # to check for existence. they will now be passed individually to # the checkout/update subroutines. this will take up more memory, # but it should make it easier if the user decides to add another # component from the same repository later my @checkouts = split( /\s+/m, $rec{"CHECKOUT"} ); foreach my $checkout (@checkouts) { }}} in line 565 which however causes the test to run for every single CHECKOUT item. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1439> 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] #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] #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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Trac November 2014