Trac April 2014

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157 discussions

[Einstein Toolkit] #1548: stdout redirection in multithreading scenario
by Einstein Toolkit 22 May '14

22 May '14

#1548: stdout redirection in multithreading scenario ---------------------------------+------------------------------------------ Reporter: gzheng@… | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: development version Keywords: stdout redirection | ---------------------------------+------------------------------------------ Current stdout redirection scheme implemented in CommandLine.c:CCTKi_CommandLineFinished() (which redirects stdout to a file or /dev/null based on myproc) does not work on multithreaded MPI (e.g AMPI), because it redirects all output (from all threads in a process). That is, all MPI ranks in a process will be mistakenly directly to one file, or if redirecting to /dev/null, there will be simply no output. It may be possible to implement a cctk_printf function, which checks myproc and manage the output for each thread. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1548> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1302: Reduce time spent in deciding not to do output.
by Einstein Toolkit 21 May '14

21 May '14

#1302: Reduce time spent in deciding not to do output. --------------------------------------+------------------------------------- Reporter: diener | Owner: eschnett Type: enhancement | Status: new Priority: major | Milestone: Component: Carpet | Version: development version Keywords: performance optimization | --------------------------------------+------------------------------------- I noticed, during some scaling tests, that for my code a significant amount of time was spent by CarpetIOASCII, even though I only had it activated and didn't actually request any output. The reason is that in order to figure out whether to do output or not, there is a loop over all grid variables and a routine (TimeToOutput) is called. In this routine there is a check if the out_dir and out_vars parameters have been steered and if so update some internal data structures. It should be sufficient to do this before entering the loop over grid variables. The same issue is present in CarpetIOScalar and CarpetIOHDF5. The attached patches for CarpetIOASCII, CarpetIOScalar and CarpetIOHDF5 moves this check outside of the loop over grid variables and in addition bypasses the loop completely if the out_vars parameter string is the empty string. Note that the code where I noticed this problem uses large vectors of 1D grid arrays, and it turns out that Cactus counts each vector element as a distinct grid variables and the length of the loop over grid variables in my case was close to 100.000, which might explain why nobody has noticed this before. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1302> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1554: Want to define constants in parameter files
by Einstein Toolkit 21 May '14

21 May '14

#1554: Want to define constants in parameter files -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Cactus | Version: development version Keywords: | -------------------------+-------------------------------------------------- I would like to define constants in parameter files, such as: {{{ $rho = 1 grid::dx = 1.0/$rho IOASCII::out_every = 10*$rho }}} The expansion of expressions is already implemented, but is limited to parameters. Being able to define constants would be very cool. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1554> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1597: use gsissh when connecting to bluewaters
by Einstein Toolkit 20 May '14

20 May '14

#1597: use gsissh when connecting to bluewaters -------------------------+-------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: enhancement | Status: new Priority: major | Milestone: Component: SimFactory | Version: development version Keywords: | -------------------------+-------------------------------------------------- the attached patch copies functionality from kraken.ini to use in bluewaters.ini and to have it use a myproxy instance to avoid having to enter the password each time one connects to bluewaters. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1597> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1468: Building a configuration with just the MPI thorn fails
by Einstein Toolkit 20 May '14

20 May '14

#1468: Building a configuration with just the MPI thorn fails ----------------------+----------------------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: optional | Milestone: Component: Cactus | Version: development version Keywords: | ----------------------+----------------------------------------------------- If I build a Cactus configuration with a thornlist containing just the MPI thorn (i.e no driver or any other thorns), the compilation fails with {{{ COMPILING /Users/ian/Cactus/EinsteinToolkit/src/comm/CactusDefaultComm.c In file included from /Users/ian/Cactus/EinsteinToolkit/configs/mpitest/build/Cactus/comm/CactusDefaultComm.c:33: /opt/local/include/openmpi/mpi.h:367: error: wrong number of arguments specified for ‘__deprecated__’ attribute }}} Building the flesh without the MPI thorn works OK. This is on Mac OS with MPI from MacPorts. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1468> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1207: Einstein toolkit sites with invalid security certificates
by Einstein Toolkit 19 May '14

19 May '14

#1207: Einstein toolkit sites with invalid security certificates -------------------------------------+-------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit website | Version: Keywords: | -------------------------------------+-------------------------------------- https://einsteintoolkit.org exists but has an invalid security certificate (http://www.sslshopper.com/ssl-checker.html#hostname=einsteintoolkit.org). I don't think we need SSL/TLS on this server. It should either be disabled or a valid certificate used. The same applies to https://cactuscode.org (http://www.sslshopper.com/ssl- checker.html#hostname=cactuscode.org). Note that Frank's page (http://www.cct.lsu.edu/~knarf/cgi-bin/monitor.cgi) reports these certificates as self-signed; they are also expired. Self- signed certificates on public websites are bad: they encourage people to click through the warnings. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1207> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1546: LoopControl commit e0ddb732 contains Fortran 2003 code
by Einstein Toolkit 19 May '14

19 May '14

#1546: LoopControl commit e0ddb732 contains Fortran 2003 code --------------------+------------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: development version Keywords: | --------------------+------------------------------------------------------- commit e0ddb732 "LoopControl: Rewrite" from Wed Jan 16 14:46:17 2013 -0500 introduces Fortran 2003 features (namely {{{bind(C)}}} in loopcontrol_types.F90. This fails to compile with gfortran 4.1.2 (the default gfortran on RH 5 machines, which are still around). David Radice stumbled oppon this. We had 2003 code in Carpet before, in ticket #670. At that point we modified the code to compile with gfortran 4.1.2 and removed the advanced features. Since gfortran 4.1.2 is by now 4 years old and none of our production option lists show the problem, I think we are finally ready to use some F2003 features in the code. We should then document this in the release notes, either for Cactus if we want to make this choice system wide or only for the ET/Carpet if we want to support running eg PUGH with only F90 around. We already require C99 in the Cactus flesh. Possibly we should take this discussion to cactus-devel. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1546> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1373: GRHydro::tov_slowsector test fails in ET_2013_05
by Einstein Toolkit 19 May '14

19 May '14

#1373: GRHydro::tov_slowsector test fails in ET_2013_05 -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: GRHydro | -----------------------------------+---------------------------------------- Most likely due to intel vs. gcc compiler issues. This ticket to serve as a reminder to fix this and to collect information known about this issue. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1373> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1378: provide equivalent of fprintf(stderr, "%s\n", msg) in Fortran
by Einstein Toolkit 19 May '14

19 May '14

#1378: provide equivalent of fprintf(stderr, "%s\n", msg) in Fortran -------------------------+-------------------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: | -------------------------+-------------------------------------------------- Currently to write out multi-line error messages in Fortran we use multiple calls to CCTK_WARN(1, warnline) followed possibly by a CCTK_ERROR(errline). Each of the level 1 warnings (given certain settings of the Cactus parameters) prints the source file location and other information to screen, thus cluttering the error output. A typical error message might look like this: {{{ WARNING level 1 in thorn GRHydro processor 179 host nid03278 (line 386 of GRHydro_Prim2Con.F90): -> EOS error in prim2con_hot: WARNING level 1 in thorn GRHydro processor 179 host nid03278 (line 388 of GRHydro_Prim2Con.F90): -> 64897 22 37 31 -1.440000E+00 -8.496000E+01 -1.296000E+01 8.595485E+01 WARNING level 1 in thorn GRHydro processor 179 host nid03278 (line 390 of GRHydro_Prim2Con.F90): -> 1.228064E-09 -8.644951E-03 -5.842300E-01 4.789413E-01 WARNING level 1 in thorn GRHydro processor 179 host nid03278 (line 392 of GRHydro_Prim2Con.F90): -> code: 106 WARNING level 1 in thorn GRHydro processor 179 host nid03278 (line 394 of GRHydro_Prim2Con.F90): -> reflevel: 0 WARNING level 1 in thorn GRHydro processor 179 host nid03278 (line 386 of GRHydro_Prim2Con.F90): -> EOS error in prim2con_hot: WARNING level 1 in thorn GRHydro processor 179 host nid03278 (line 388 of GRHydro_Prim2Con.F90): -> 64897 23 37 31 1.440000E+00 -8.496000E+01 -1.296000E+01 8.595485E+01 WARNING level 1 in thorn GRHydro processor 179 host nid03278 (line 390 of GRHydro_Prim2Con.F90): -> 1.227982E-09 -8.644755E-03 -5.798389E-01 4.789407E-01 WARNING level 1 in thorn GRHydro processor 179 host nid03278 (line 392 of GRHydro_Prim2Con.F90): -> code: 106 WARNING level 1 in thorn GRHydro processor 179 host nid03278 (line 394 of GRHydro_Prim2Con.F90): -> reflevel: 0 WARNING level 1 in thorn GRHydro processor 179 host nid03278 (line 166 of GRHydro_Eigenproblem.F90): -> EOS ERROR in eigenvalues_hot WARNING level 1 in thorn GRHydro processor 179 host nid03278 (line 168 of GRHydro_Eigenproblem.F90): -> keyerr: 668 keytemp: 0 WARNING level 0 in thorn GRHydro processor 179 host nid03278 (line 170 of GRHydro_Eigenproblem.F90): -> 1.228064E-09 -8.644951E-03 -5.842300E-01 4.789413E-01 5.668696E-04 cactus_sim: Cactus/arrangements/Carpet/Carpet/src/helpers.cc:314: int Carpet::Abort(const cGH*, int): Assertion `0' failed. Rank 179 with PID 13388 received signal 6 }}} with errors from multiple MPI processes possibly intersecting each other. It would be useful to provide a subroutine equivalent to {{{ subroutine CCTK_WARN_SHORT(msg) character*(*) :: msg write (stderr,'(a)') msg end subroutine }}} (name is up for discussion) that outputs only "msg" to stderr (and the warning listener registered in the flesh) without prepending the file information output. A similar routine might be offered for C (in WARN and VWarn flavors) both for symmetry reasons and to have the message pass the warning listeners, though in C one can usually get away with a single CCTK_VWarn and a very long format string. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1378> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1551: Strange warnings at startup
by Einstein Toolkit 19 May '14

19 May '14

#1551: Strange warnings at startup ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: | ----------------------+----------------------------------------------------- I see this warning multiple times at startup on Blue Waters: {{{ ^[[1mWARNING[L1,P0] (Flesh):^[[0m Invalid end }}} This is apparently output by the routine Util_IntInRange or Util_DoubleInRange. This happens for the parameter file simfactory/etc/parfiles/submit.par. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1551> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac April 2014