From latife at astro.rug.nl Mon Nov 3 10:34:31 2008 From: latife at astro.rug.nl (M.A. Latife) Date: Mon, 03 Nov 2008 17:34:31 +0100 Subject: [FLASH-USERS] non convergence in Riemann subroutine Message-ID: <490F2817.6060300@astro.rug.nl> Hi Dear All, I am running 3-D simulations including hydro + particles + cosmology + eos + gravity + cooling. My simulations crash after some time (1.0E15) and give the following error. it seems me that there is something going wrong in Riemann.F90 with pressure. What are possible causes of this problem? How can i avoid this problem? Any idea Kind Regards Latif Nonconvergence in subroutine rieman! Processor, block = 7 20 Zone index = 5 Transverse index = 6 5 Zone center = 1.170820312500000E+025 Sweep direction = x Iterations tried = 27 Pressure error = 5.45416055415388 pL = 4.117027057197573E-022 pR = 3.938433206566095E-022 uL = -12152456.2730107 uR = -10892043.1131041 cL = 1.041411422316767E-026 cR = 1.028454571441834E-026 gamma_eL = 1.00765479619375 gamma_eR = 1.00766156258855 gamma_cL = 1.00765479619375 gamma_cR = 1.00766156258855 Iteration history: n p* 1 0.100000000000E-29 2 0.178214204180E-25 3 0.191075724471E-27 4 0.377139479396E-27 5 0.178214203785E-25 6 0.559316960640E-27 7 0.737728667286E-27 8 0.178214203773E-25 9 0.912490167868E-27 10 0.108371234987E-26 11 0.178214204060E-25 12 0.125150165427E-26 13 0.141596029646E-26 14 0.178214203879E-25 15 0.157718647365E-26 16 0.173527456037E-26 17 0.178214204639E-25 18 0.189031529261E-26 19 0.204239594204E-26 20 0.178214204634E-25 21 0.219160047921E-26 22 0.233800972837E-26 23 0.178214204400E-25 24 0.248170151347E-26 25 0.262275079601E-26 26 0.178214204915E-25 27 0.276122980549E-26 Terminating execution. From tplewa at fsu.edu Mon Nov 3 12:33:29 2008 From: tplewa at fsu.edu (Tomasz Plewa) Date: Mon, 03 Nov 2008 13:33:29 -0500 Subject: [FLASH-USERS] non convergence in Riemann subroutine In-Reply-To: <490F2817.6060300@astro.rug.nl> References: <490F2817.6060300@astro.rug.nl> Message-ID: <490F43F9.8020802@fsu.edu> Latif - The gammas close to 1 are a possible cause of this failure. What equation of state are you using? Tomek -- M.A. Latife wrote: > Hi > Dear All, > I am running 3-D simulations including hydro + particles + cosmology > + eos + gravity + cooling. My simulations crash after some time > (1.0E15) and give the following error. it seems me that there is > something going wrong in Riemann.F90 with pressure. What are possible > causes of this problem? How can i avoid this problem? > Any idea > Kind Regards > Latif > Nonconvergence in subroutine rieman! > > Processor, block = 7 20 > Zone index = 5 > Transverse index = 6 5 > Zone center = 1.170820312500000E+025 > Sweep direction = x > Iterations tried = 27 > Pressure error = 5.45416055415388 > pL = 4.117027057197573E-022 pR = 3.938433206566095E-022 > uL = -12152456.2730107 uR = -10892043.1131041 > cL = 1.041411422316767E-026 cR = 1.028454571441834E-026 > gamma_eL = 1.00765479619375 gamma_eR = 1.00766156258855 > gamma_cL = 1.00765479619375 gamma_cR = 1.00766156258855 > Iteration history: > > n p* > 1 0.100000000000E-29 > 2 0.178214204180E-25 > 3 0.191075724471E-27 > 4 0.377139479396E-27 > 5 0.178214203785E-25 > 6 0.559316960640E-27 > 7 0.737728667286E-27 > 8 0.178214203773E-25 > 9 0.912490167868E-27 > 10 0.108371234987E-26 > 11 0.178214204060E-25 > 12 0.125150165427E-26 > 13 0.141596029646E-26 > 14 0.178214203879E-25 > 15 0.157718647365E-26 > 16 0.173527456037E-26 > 17 0.178214204639E-25 > 18 0.189031529261E-26 > 19 0.204239594204E-26 > 20 0.178214204634E-25 > 21 0.219160047921E-26 > 22 0.233800972837E-26 > 23 0.178214204400E-25 > 24 0.248170151347E-26 > 25 0.262275079601E-26 > 26 0.178214204915E-25 > 27 0.276122980549E-26 > > Terminating execution. > -------------- next part -------------- A non-text attachment was scrubbed... Name: tplewa.vcf Type: text/x-vcard Size: 296 bytes Desc: not available Url : http://flash.uchicago.edu/pipermail/flash-users/attachments/20081103/6b6fa0cc/attachment.vcf From mateuszr at umich.edu Fri Nov 7 18:08:40 2008 From: mateuszr at umich.edu (Mateusz Ruszkowski) Date: Fri, 7 Nov 2008 19:08:40 -0500 (EST) Subject: [FLASH-USERS] restarting and particle file In-Reply-To: <490F43F9.8020802@fsu.edu> References: <490F2817.6060300@astro.rug.nl> <490F43F9.8020802@fsu.edu> Message-ID: Hi all, I noticed that restarting the code makes it write particle files every timestep. Doing the obvious (i.e., changing the parameter file) does not help. Has anybody encountered this problem? I am using FLASH3.1. thanks, Mateusz From dubey at flash.uchicago.edu Tue Nov 11 16:06:57 2008 From: dubey at flash.uchicago.edu (Anshu Dubey) Date: Tue, 11 Nov 2008 16:06:57 -0600 Subject: [FLASH-USERS] FLASH presentation at SC08 Message-ID: <5b942a610811111406y587b5dddkbe300efc776292db@mail.gmail.com> There will be a presentation "FLASH code: What it can do for you" on Wed 11/19 11:00-11:45 in the ASC booth at SC08. After the presentation, members of the Flash Code group will be around to answer questions/ help users. We will also be available at other times by appointment. The FLASH Code group. From seyit at astro.rug.nl Wed Nov 12 09:08:36 2008 From: seyit at astro.rug.nl (Seyit Hocuk) Date: Wed, 12 Nov 2008 16:08:36 +0100 Subject: [FLASH-USERS] FLASH presentation at SC08 In-Reply-To: <5b942a610811111406y587b5dddkbe300efc776292db@mail.gmail.com> References: <5b942a610811111406y587b5dddkbe300efc776292db@mail.gmail.com> Message-ID: <491AF174.60605@astro.rug.nl> Hi, Too bad it was announced so late, otherwise I surely would have wanted to attend it. I really like that there are such 'workshops' about FLASH and hope there will be much more in the future. I will attend them if I have the chance. Kind Regards, Seyit Anshu Dubey wrote: > There will be a presentation "FLASH code: What it can do for you" on > Wed 11/19 11:00-11:45 in the ASC booth at SC08. After the presentation, > members of the Flash Code group will be around to answer questions/ > help users. We will also be available at other times by appointment. > > The FLASH Code group. > From hudson at mcs.anl.gov Mon Nov 17 10:51:09 2008 From: hudson at mcs.anl.gov (Randy Hudson) Date: Mon, 17 Nov 2008 10:51:09 -0600 Subject: [FLASH-USERS] Fwd: [visit-users] VisIt 1.11 released References: <7c0g87$tojqh@nspiron-2.llnl.gov> Message-ID: New visit available. ALso, check the release notes (see link below). Begin forwarded message: > From: Eric Brugger > Date: November 14, 2008 5:18:23 PM CST > To: visit-users at email.ornl.gov > Subject: [visit-users] VisIt 1.11 released > Reply-To: VisIt software users community > > > > Hi all, > > VisIt 1.11 is now available. > > Source code and prebuilt executables are available on the visit web > site > (https://visit.llnl.gov/). > > Changes for the 1.11 release can be found at > > https://visit.llnl.gov/relnotes1.11.0.html. > > Eric > > -- > List subscription information: https://email.ornl.gov/mailman/listinfo/visit-users > Searchable list archives: https://email.ornl.gov/pipermail/visit-users > Randy. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://flash.uchicago.edu/pipermail/flash-users/attachments/20081117/cededc0f/attachment.html From mateuszr at umich.edu Mon Nov 17 12:49:31 2008 From: mateuszr at umich.edu (Mateusz Ruszkowski) Date: Mon, 17 Nov 2008 13:49:31 -0500 (EST) Subject: [FLASH-USERS] truncation errors and restarting In-Reply-To: References: Message-ID: Hi, I am restarting from a checkpoint file a run that crashed due to a segmentation fault. For many steps after the restart the code behaves *exactly* the same way as before prior to the crash. However, at some point the timestep changes by 10% in one step. The restarted run is now past the point where the code crashed before and is now running normally. I understand that it may be very difficult to diagnose a problem like this one. But I am wondering if it is possible that some tiny truncation errors in the checkpoint file eventually made code behave sightly differently (e.g., different switches got activated, etc) which in turn prevented the crash due to the segmentation fault. Is this possible ? Mateusz P.S. this is what happens around the time the timestep changes (previous timesteps were identical) Old: [ 11-17-2008 03:59:53.253 ] [gr_hgSolve]: gr_hgSolve: ite 4: norm(residual)/norm(src) = 1.445309E-06 [ 11-17-2008 03:59:53.289 ] [mpi_amr_comm_setup]: buffer_dim_send=291565, buffer_dim_recv=218221 [ 11-17-2008 03:59:53.816 ] [mpi_amr_comm_setup]: buffer_dim_send=232373, buffer_dim_recv=188625 [ 11-17-2008 03:59:54.186 ] [mpi_amr_comm_setup]: buffer_dim_send=227937, buffer_dim_recv=188625 [ 11-17-2008 03:59:54.692 ] [mpi_amr_comm_setup]: buffer_dim_send=227353, buffer_dim_recv=188625 [ 11-17-2008 03:59:56.718 ] [gr_hgSolve]: gr_hgSolve: ite 5: norm(residual)/norm(src) = 1.673032E-07 [ 11-17-2008 03:59:58.194 ] step: n=1029 t=7.484192E+05 dt=2.140401E+02 [ 11-17-2008 03:59:58.536 ] [mpi_amr_comm_setup]: buffer_dim_send=5646649, buffer_dim_recv=4801841 [ 11-17-2008 04:00:07.804 ] [mpi_amr_comm_setup]: buffer_dim_send=1310137, buffer_dim_recv=1107121 [ 11-17-2008 04:00:13.468 ] [mpi_amr_comm_setup]: buffer_dim_send=4375321, buffer_dim_recv=3722705 Restarted: [ 11-17-2008 11:29:55.951 ] [gr_hgSolve]: gr_hgSolve: ite 4: norm(residual)/norm(src) = 1.445309E-06 [ 11-17-2008 11:29:55.986 ] [mpi_amr_comm_setup]: buffer_dim_send=291565, buffer_dim_recv=218221 [ 11-17-2008 11:29:56.550 ] [mpi_amr_comm_setup]: buffer_dim_send=232373, buffer_dim_recv=188625 [ 11-17-2008 11:29:56.921 ] [mpi_amr_comm_setup]: buffer_dim_send=227937, buffer_dim_recv=188625 [ 11-17-2008 11:29:57.454 ] [mpi_amr_comm_setup]: buffer_dim_send=227353, buffer_dim_recv=188625 [ 11-17-2008 11:29:59.433 ] [gr_hgSolve]: gr_hgSolve: ite 5: norm(residual)/norm(src) = 1.673031E-07 [ 11-17-2008 11:30:05.081 ] step: n=1029 t=7.484192E+05 dt=2.506123E+02 [ 11-17-2008 11:30:05.436 ] [mpi_amr_comm_setup]: buffer_dim_send=5646649, buffer_dim_recv=4801841 [ 11-17-2008 11:30:14.690 ] [mpi_amr_comm_setup]: buffer_dim_send=1310137, buffer_dim_recv=1107121 [ 11-17-2008 11:30:20.366 ] [mpi_amr_comm_setup]: buffer_dim_send=4375321, buffer_dim_recv=3722705 From jfg at ucolick.org Wed Nov 19 10:50:57 2008 From: jfg at ucolick.org (James Guillochon) Date: Wed, 19 Nov 2008 08:50:57 -0800 Subject: [FLASH-USERS] Burn and MA28 Fix Message-ID: <492443F1.3020504@ucolick.org> Hi guys, So I had been getting singularity errors in the MA28 library when using the Burn unit in Flash 3.1. Then I realized the issue: The Makefile for the MA28 library does not use the same fortran flag variables as the main Makefile.h specifies (FFLAGS_OPT, etc), and was being compiled (by default) without 64-bit arithmetic. I just copied the flags in FFLAGS_OPT from my site-specific Makefile.h (which includes -r8 and -real_size 64) into the MA28 Makefile, and now I get no more errors. So I think that future releases should alter the MA28 Makefile such that the compile rule for .F90 files includes these flags, either by using the supplied FFLAGS variables or by just appending them to rule directly. -- James Guillochon Department of Astronomy & Astrophysics University of California, Santa Cruz jfg at ucolick.org From cdaley at flash.uchicago.edu Wed Nov 19 15:54:28 2008 From: cdaley at flash.uchicago.edu (Chris Daley) Date: Wed, 19 Nov 2008 15:54:28 -0600 Subject: [FLASH-USERS] Burn and MA28 Fix In-Reply-To: <492443F1.3020504@ucolick.org> References: <492443F1.3020504@ucolick.org> Message-ID: <49248B14.6090806@flash.uchicago.edu> Hi James, I'm sorry that you have run into this error. I remember having the exact same error a few months ago. I'm a bit confused why it has happened again? When I discovered this problem I created a python source file at lib/ma28/libinfo.py which is called by the setup script. In this file I generate a build script on the fly named build.csh which calls the Makefile with a variable containing the extra compilation flags (including e.g. 64 bit reals). The extra flags come from your Makefile.h (either FFLAGS_DEBUG, FFLAGS_TEST, FFLAGS_OPT depending on how you setup), and the Makefile is at /lib/ma28/source/Makefile. e.g. In my Makefile .h: FFLAGS_OPT = -c --o2 --tp4 -CcdRR8 [cdaley at cetus ma28]$ more build.csh #!/bin/csh # Dont forget to make this file executable! cd source gmake clean gmake -f Makefile EXTRA_FFLAGS=" -c --o2 --tp4 -CcdRR8" cd .. What does your build.csh look like? Chris James Guillochon wrote: > Hi guys, > > So I had been getting singularity errors in the MA28 library when > using the Burn unit in Flash 3.1. Then I realized the issue: The > Makefile for the MA28 library does not use the same fortran flag > variables as the main Makefile.h specifies (FFLAGS_OPT, etc), and was > being compiled (by default) without 64-bit arithmetic. I just copied > the flags in FFLAGS_OPT from my site-specific Makefile.h (which > includes -r8 and -real_size 64) into the MA28 Makefile, and now I get > no more errors. > > So I think that future releases should alter the MA28 Makefile such > that the compile rule for .F90 files includes these flags, either by > using the supplied FFLAGS variables or by just appending them to rule > directly. >