Hi all. I'd like to visualise some 3D data produced by an initial-data run of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as recommended by cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the following error:
--------------------------------------------------------------------------- ---- The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open "/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol_cou lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer. --------------------------------------------------------------------------- ----
I have no idea whether the file is corrupted, but wanted to know: is the CarpetHDF5 plugin up-to-date with the output of Maxwell's CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
Thanks,
Bernard
---------------------------------------------------------------------------
On 10 Apr 2012, at 22:21, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Hi all. I'd like to visualise some 3D data produced by an initial-data run of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as recommended by cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the following error:
The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open "/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol_cou lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
I have no idea whether the file is corrupted, but wanted to know: is the CarpetHDF5 plugin up-to-date with the output of Maxwell's CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
One problem can come from Visit trying to open too many files for the maximum open file limit of your OS. Mac OS, for example, has a very small limit. Try changing this with ulimit. But ultimately, you should try to find the actual error message. I think there is an option for Visit to output the errors to a file, but it's so long since I've used Visit that I don't remember. Probably someone else can fill that in...
Hello all,
One problem can come from Visit trying to open too many files for the maximum open file limit of your OS. Mac OS, for example, has a very small limit. Try changing this with ulimit. But ultimately, you should try to find the actual error message. I think there is an option for Visit to output the errors to a file, but it's so long since I've used Visit that I don't remember. Probably someone else can fill that in...
Well it has -debug options... My first try (in case you have not done so yet) would be to start visit from a command line. I then spits out errors to stderr.
If it complains about mismatching HDF5 libraries, then it will also tell you how to work around this (the good fix is to compile with the version of HDF5 inside VisIt, there are include and lib directories inside of the VisIt install, the quick fix is an environment variable HDF5_INGORE_VERSION_CHECK or so).
Yours, Roland
Hi Ian.
I'll look for a logfile, but there was nothing generated in my ~/.visit that I could see.
Which reminds me: can frequent Visit/CarpetHDF5 users confirm for me where they get (a) Visit, and (b) CarpetHDF5? For me the answers are:
(a) the "Mac OS X - Intel 64 bit" binary from here: https://wci.llnl.gov/codes/visit/executables.html
(b) the cactuscode VizTools trunk via svn: svn co https://svn.cactuscode.org/VizTools/CarpetHDF5/trunk/ CarpetHDF5
The instructions in the latter's README.txt seem a bit out of date, which made me suspicious. The lines about "updating the paths to the HDF5 library", for instance:
install_name_tool -change '@executable_path/../lib/libhdf5.dylib' '/usr/local/lib/libhdf5.1.dylib' ~/.visit/darwin-i386/plugins/databases/libEvisitCarpetHDF5Database_ser.dyli b
Now my 64-bit installation generates three subdirectories in ~/.visit: "2.4.2", "darwin-i386", and "darwin-x86_64". Of these, only "2.4.2" had any content in the "plugins/databases/" subdirectory, and these dylibs were *similar but not identical* in name to what's mentioned in the README (e.g., libECarpetHDF5Database_ser.dylib rather than libEvisitCarpetHDF5Database_ser.dylib).
So ... should I be using a different version of Visit (older, 32-bit, etc.)?
Bernard
On 4/10/12 4:24 PM, "Ian Hinder" ian.hinder@aei.mpg.de wrote:
On 10 Apr 2012, at 22:21, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Hi all. I'd like to visualise some 3D data produced by an initial-data run of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as recommended by cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the following error:
--
The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open
"/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol_c ou lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
--
I have no idea whether the file is corrupted, but wanted to know: is the CarpetHDF5 plugin up-to-date with the output of Maxwell's CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
One problem can come from Visit trying to open too many files for the maximum open file limit of your OS. Mac OS, for example, has a very small limit. Try changing this with ulimit. But ultimately, you should try to find the actual error message. I think there is an option for Visit to output the errors to a file, but it's so long since I've used Visit that I don't remember. Probably someone else can fill that in...
-- Ian Hinder http://numrel.aei.mpg.de/people/hinder
On 11 Apr 2012, at 19:10, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Hi Ian.
I'll look for a logfile, but there was nothing generated in my ~/.visit that I could see.
Which reminds me: can frequent Visit/CarpetHDF5 users confirm for me where they get (a) Visit, and (b) CarpetHDF5? For me the answers are:
(a) the "Mac OS X - Intel 64 bit" binary from here: https://wci.llnl.gov/codes/visit/executables.html
(b) the cactuscode VizTools trunk via svn: svn co https://svn.cactuscode.org/VizTools/CarpetHDF5/trunk/ CarpetHDF5
The instructions in the latter's README.txt seem a bit out of date, which made me suspicious. The lines about "updating the paths to the HDF5 library", for instance:
Is the Carpet VisIt plugin part of the ET? If it is, then we should make sure the documentation (i.e. the README) is up-to-date for each ET release. If not, we should probably do it anyway :)
install_name_tool -change '@executable_path/../lib/libhdf5.dylib' '/usr/local/lib/libhdf5.1.dylib' ~/.visit/darwin-i386/plugins/databases/libEvisitCarpetHDF5Database_ser.dyli b
Now my 64-bit installation generates three subdirectories in ~/.visit: "2.4.2", "darwin-i386", and "darwin-x86_64". Of these, only "2.4.2" had any content in the "plugins/databases/" subdirectory, and these dylibs were *similar but not identical* in name to what's mentioned in the README (e.g., libECarpetHDF5Database_ser.dylib rather than libEvisitCarpetHDF5Database_ser.dylib).
So ... should I be using a different version of Visit (older, 32-bit, etc.)?
Bernard
On 4/10/12 4:24 PM, "Ian Hinder" ian.hinder@aei.mpg.de wrote:
On 10 Apr 2012, at 22:21, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Hi all. I'd like to visualise some 3D data produced by an initial-data run of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as recommended by cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the following error:
--
The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open
"/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol_c ou lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
--
I have no idea whether the file is corrupted, but wanted to know: is the CarpetHDF5 plugin up-to-date with the output of Maxwell's CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
One problem can come from Visit trying to open too many files for the maximum open file limit of your OS. Mac OS, for example, has a very small limit. Try changing this with ulimit. But ultimately, you should try to find the actual error message. I think there is an option for Visit to output the errors to a file, but it's so long since I've used Visit that I don't remember. Probably someone else can fill that in...
-- Ian Hinder http://numrel.aei.mpg.de/people/hinder
On Wed, Apr 11, 2012 at 1:20 PM, Ian Hinder ian.hinder@aei.mpg.de wrote:
On 11 Apr 2012, at 19:10, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Hi Ian.
I'll look for a logfile, but there was nothing generated in my ~/.visit that I could see.
Which reminds me: can frequent Visit/CarpetHDF5 users confirm for me where they get (a) Visit, and (b) CarpetHDF5? For me the answers are:
(a) the "Mac OS X - Intel 64 bit" binary from here: https://wci.llnl.gov/codes/visit/executables.html
(b) the cactuscode VizTools trunk via svn: svn co https://svn.cactuscode.org/VizTools/CarpetHDF5/trunk/ CarpetHDF5
The instructions in the latter's README.txt seem a bit out of date, which made me suspicious. The lines about "updating the paths to the HDF5 library", for instance:
Is the Carpet VisIt plugin part of the ET? If it is, then we should make sure the documentation (i.e. the README) is up-to-date for each ET release. If not, we should probably do it anyway :)
I believe it is not. The plan is instead to have it be included with VisIt, and be available by default. For some reason, this seems to take a few more years that we initially expected.
-erik
On Wed, Apr 11, 2012 at 1:20 PM, Ian Hinder ian.hinder@aei.mpg.de wrote:
On 11 Apr 2012, at 19:10, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF
MARYLAND BALTIMORE COUNTY] wrote:
Hi Ian.
I'll look for a logfile, but there was nothing generated in my ~/.visit that I could see.
Which reminds me: can frequent Visit/CarpetHDF5 users confirm for me where they get (a) Visit, and (b) CarpetHDF5? For me the answers are:
(a) the "Mac OS X - Intel 64 bit" binary from here: https://wci.llnl.gov/codes/visit/executables.html
(b) the cactuscode VizTools trunk via svn: svn co https://svn.cactuscode.org/VizTools/CarpetHDF5/trunk/ CarpetHDF5
The instructions in the latter's README.txt seem a bit out of date, which made me suspicious. The lines about "updating the paths to the HDF5
library", for instance:
Is the Carpet VisIt plugin part of the ET? If it is, then we should make sure the documentation (i.e. the README) is up-to-date for each ET release. If not, we should probably do it anyway :)
I believe it is not. The plan is instead to have it be included with VisIt, and be available by default. For some reason, this seems to take a few more years that we initially expected.
I have send Hank Childs a tarball of the most recent version of the plugin a while ago and he promised to put it to the VisIt SVN repository. However, it is still not part of the latest release. I probably should contact him again.
Christian
Hi Ian, Christian.
I'd be great if the plugin became part of VisIt itself, since that would remove some possible mismatches in HDF5 library versions (as well as avoiding the need for separate compilation).
In the mean time, what I *really* need is a version of the CarpetHDF5 plugin with up-to-date installation instructions that is known to work with the *current* VisIt release (2.4.2). I tried moving back to VisIt 2.3.2 to match what Bruno mentioned, but it didn't work any better.
Has anyone installed VisIt + CarpetHDF5 on a Mac from scratch *recently*?
Bernard
On 4/11/12 1:20 PM, "Ian Hinder" ian.hinder@aei.mpg.de wrote:
On 11 Apr 2012, at 19:10, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Hi Ian.
I'll look for a logfile, but there was nothing generated in my ~/.visit that I could see.
Which reminds me: can frequent Visit/CarpetHDF5 users confirm for me where they get (a) Visit, and (b) CarpetHDF5? For me the answers are:
(a) the "Mac OS X - Intel 64 bit" binary from here: https://wci.llnl.gov/codes/visit/executables.html
(b) the cactuscode VizTools trunk via svn: svn co https://svn.cactuscode.org/VizTools/CarpetHDF5/trunk/ CarpetHDF5
The instructions in the latter's README.txt seem a bit out of date, which made me suspicious. The lines about "updating the paths to the HDF5 library", for instance:
Is the Carpet VisIt plugin part of the ET? If it is, then we should make sure the documentation (i.e. the README) is up-to-date for each ET release. If not, we should probably do it anyway :)
Bernard,
On Apr 11, 2012, at 11:10 AM, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Which reminds me: can frequent Visit/CarpetHDF5 users confirm for me where they get (a) Visit, and (b) CarpetHDF5? For me the answers are:
(a) the "Mac OS X - Intel 64 bit" binary from here: https://wci.llnl.gov/codes/visit/executables.html
I also use the 64 bit binary (version 2.3.2 in my case).
(b) the cactuscode VizTools trunk via svn: svn co https://svn.cactuscode.org/VizTools/CarpetHDF5/trunk/ CarpetHDF5
yes, this is the correct repository. I didn't need to update the path in my case. I just followed the standard installation instructions and it worked without problems.
Cheers, Bruno
The instructions in the latter's README.txt seem a bit out of date, which made me suspicious. The lines about "updating the paths to the HDF5 library", for instance:
install_name_tool -change '@executable_path/../lib/libhdf5.dylib' '/usr/local/lib/libhdf5.1.dylib' ~/.visit/darwin-i386/plugins/databases/libEvisitCarpetHDF5Database_ser.dyli b
Now my 64-bit installation generates three subdirectories in ~/.visit: "2.4.2", "darwin-i386", and "darwin-x86_64". Of these, only "2.4.2" had any content in the "plugins/databases/" subdirectory, and these dylibs were *similar but not identical* in name to what's mentioned in the README (e.g., libECarpetHDF5Database_ser.dylib rather than libEvisitCarpetHDF5Database_ser.dylib).
So ... should I be using a different version of Visit (older, 32-bit, etc.)?
Bernard
On 4/10/12 4:24 PM, "Ian Hinder" ian.hinder@aei.mpg.de wrote:
On 10 Apr 2012, at 22:21, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Hi all. I'd like to visualise some 3D data produced by an initial-data run of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as recommended by cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the following error:
--
The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open
"/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol_c ou lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
--
I have no idea whether the file is corrupted, but wanted to know: is the CarpetHDF5 plugin up-to-date with the output of Maxwell's CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
One problem can come from Visit trying to open too many files for the maximum open file limit of your OS. Mac OS, for example, has a very small limit. Try changing this with ulimit. But ultimately, you should try to find the actual error message. I think there is an option for Visit to output the errors to a file, but it's so long since I've used Visit that I don't remember. Probably someone else can fill that in...
-- Ian Hinder http://numrel.aei.mpg.de/people/hinder
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Dr. Bruno Giacomazzo JILA - University of Colorado 440 UCB Boulder, CO 80309 USA
Tel. : +1 303-492-0389 Fax : +1 303-492-5235 email : bruno.giacomazzo@jila.colorado.edu web: http://www.brunogiacomazzo.org
---------------------------------------------------------------------- There are only 10 types of people in the world: Those who understand binary, and those who don't ----------------------------------------------------------------------
Bruno,
You are using MacPorts, right? What version of OS X do you have? I'm running Lion.
"yes, this is the correct repository. I didn't need to update the path in my case. I just followed the standard installation instructions and it worked without problems."
That hasn't been true for me -- can't get it to work even after surmounting various problems along the way -- and don't think it has for Bernard, but we'd really like to get it working!
-Scott
From: Bruno Giacomazzo <bruno.giacomazzo@jila.colorado.edumailto:bruno.giacomazzo@jila.colorado.edu> Date: Wednesday, April 11, 2012 12:36 PM To: "Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY]" <bernard.j.kelly@nasa.govmailto:bernard.j.kelly@nasa.gov> Cc: Einstein Toolkit Users <users@einsteintoolkit.orgmailto:users@einsteintoolkit.org> Subject: Re: [Users] Visit & CarpetHDF5 mismatch?
Bernard,
On Apr 11, 2012, at 11:10 AM, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Which reminds me: can frequent Visit/CarpetHDF5 users confirm for me where they get (a) Visit, and (b) CarpetHDF5? For me the answers are:
(a) the "Mac OS X - Intel 64 bit" binary from here: https://wci.llnl.gov/codes/visit/executables.html
I also use the 64 bit binary (version 2.3.2 in my case).
(b) the cactuscode VizTools trunk via svn: svn co https://svn.cactuscode.org/VizTools/CarpetHDF5/trunk/ CarpetHDF5
yes, this is the correct repository. I didn't need to update the path in my case. I just followed the standard installation instructions and it worked without problems.
Cheers, Bruno
The instructions in the latter's README.txt seem a bit out of date, which made me suspicious. The lines about "updating the paths to the HDF5 library", for instance:
install_name_tool -change '@executable_path/../lib/libhdf5.dylibmailto:'@executable_path/../lib/libhdf5.dylib' '/usr/local/lib/libhdf5.1.dylib' ~/.visit/darwin-i386/plugins/databases/libEvisitCarpetHDF5Database_ser.dyli b
Now my 64-bit installation generates three subdirectories in ~/.visit: "2.4.2", "darwin-i386", and "darwin-x86_64". Of these, only "2.4.2" had any content in the "plugins/databases/" subdirectory, and these dylibs were *similar but not identical* in name to what's mentioned in the README (e.g., libECarpetHDF5Database_ser.dylib rather than libEvisitCarpetHDF5Database_ser.dylib).
So ... should I be using a different version of Visit (older, 32-bit, etc.)?
Bernard
On 4/10/12 4:24 PM, "Ian Hinder" <ian.hinder@aei.mpg.demailto:ian.hinder@aei.mpg.de> wrote:
On 10 Apr 2012, at 22:21, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Hi all. I'd like to visualise some 3D data produced by an initial-data run of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as recommended by cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the following error:
------------------------------------------------------------------------- -- ---- The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open
"/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol_c ou lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
------------------------------------------------------------------------- -- ----
I have no idea whether the file is corrupted, but wanted to know: is the CarpetHDF5 plugin up-to-date with the output of Maxwell's CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
One problem can come from Visit trying to open too many files for the maximum open file limit of your OS. Mac OS, for example, has a very small limit. Try changing this with ulimit. But ultimately, you should try to find the actual error message. I think there is an option for Visit to output the errors to a file, but it's so long since I've used Visit that I don't remember. Probably someone else can fill that in...
-- Ian Hinder http://numrel.aei.mpg.de/people/hinder
_______________________________________________ Users mailing list Users@einsteintoolkit.orgmailto:Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Dr. Bruno Giacomazzo JILA - University of Colorado 440 UCB Boulder, CO 80309 USA
Tel. : +1 303-492-0389 Fax : +1 303-492-5235 email : bruno.giacomazzo@jila.colorado.edumailto:bruno.giacomazzo@jila.colorado.edu web: http://www.brunogiacomazzo.org
---------------------------------------------------------------------- There are only 10 types of people in the world: Those who understand binary, and those who don't ----------------------------------------------------------------------
Scott, I'm running Lion (OSX 10.7.3). I used MacPorts only to install the libraries needed by pygraph. For the VisIt CarpetHFDF5 plugin I use the hdf5 libraries installed by Fink in /sw/lib. I also needed to set HDF5_DISABLE_VERSION_CHECK=2. I'm using VisIt 2.3.2.
Cheers, Bruno
On Apr 17, 2012, at 11:17 AM, Scott Hawley wrote:
Bruno,
You are using MacPorts, right? What version of OS X do you have? I'm running Lion.
"yes, this is the correct repository. I didn't need to update the path in my case. I just followed the standard installation instructions and it worked without problems."
That hasn't been true for me -- can't get it to work even after surmounting various problems along the way -- and don't think it has for Bernard, but we'd really like to get it working!
-Scott
From: Bruno Giacomazzo bruno.giacomazzo@jila.colorado.edu Date: Wednesday, April 11, 2012 12:36 PM To: "Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY]" bernard.j.kelly@nasa.gov Cc: Einstein Toolkit Users users@einsteintoolkit.org Subject: Re: [Users] Visit & CarpetHDF5 mismatch?
Bernard,
On Apr 11, 2012, at 11:10 AM, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Which reminds me: can frequent Visit/CarpetHDF5 users confirm for me where they get (a) Visit, and (b) CarpetHDF5? For me the answers are:
(a) the "Mac OS X - Intel 64 bit" binary from here: https://wci.llnl.gov/codes/visit/executables.html
I also use the 64 bit binary (version 2.3.2 in my case).
(b) the cactuscode VizTools trunk via svn: svn co https://svn.cactuscode.org/VizTools/CarpetHDF5/trunk/ CarpetHDF5
yes, this is the correct repository. I didn't need to update the path in my case. I just followed the standard installation instructions and it worked without problems.
Cheers, Bruno
The instructions in the latter's README.txt seem a bit out of date, which made me suspicious. The lines about "updating the paths to the HDF5 library", for instance:
install_name_tool -change '@executable_path/../lib/libhdf5.dylib' '/usr/local/lib/libhdf5.1.dylib' ~/.visit/darwin-i386/plugins/databases/libEvisitCarpetHDF5Database_ser.dyli b
Now my 64-bit installation generates three subdirectories in ~/.visit: "2.4.2", "darwin-i386", and "darwin-x86_64". Of these, only "2.4.2" had any content in the "plugins/databases/" subdirectory, and these dylibs were *similar but not identical* in name to what's mentioned in the README (e.g., libECarpetHDF5Database_ser.dylib rather than libEvisitCarpetHDF5Database_ser.dylib).
So ... should I be using a different version of Visit (older, 32-bit, etc.)?
Bernard
On 4/10/12 4:24 PM, "Ian Hinder" ian.hinder@aei.mpg.de wrote:
On 10 Apr 2012, at 22:21, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Hi all. I'd like to visualise some 3D data produced by an initial-data run of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as recommended by cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the following error:
--
The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open
"/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol_c ou lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
--
I have no idea whether the file is corrupted, but wanted to know: is the CarpetHDF5 plugin up-to-date with the output of Maxwell's CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
One problem can come from Visit trying to open too many files for the maximum open file limit of your OS. Mac OS, for example, has a very small limit. Try changing this with ulimit. But ultimately, you should try to find the actual error message. I think there is an option for Visit to output the errors to a file, but it's so long since I've used Visit that I don't remember. Probably someone else can fill that in...
-- Ian Hinder http://numrel.aei.mpg.de/people/hinder
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Dr. Bruno Giacomazzo JILA - University of Colorado 440 UCB Boulder, CO 80309 USA
Tel. : +1 303-492-0389 Fax : +1 303-492-5235 email : bruno.giacomazzo@jila.colorado.edu web: http://www.brunogiacomazzo.org
There are only 10 types of people in the world: Those who understand binary, and those who don't
Dr. Bruno Giacomazzo JILA - University of Colorado 440 UCB Boulder, CO 80309 USA
Tel. : +1 303-492-0389 Fax : +1 303-492-5235 email : bruno.giacomazzo@jila.colorado.edu web: http://www.brunogiacomazzo.org
---------------------------------------------------------------------- There are only 10 types of people in the world: Those who understand binary, and those who don't ----------------------------------------------------------------------
How did you get the plugin to compile? When I run the script I getŠ
~/apps/VizTools/CarpetHDF5] % ./install make: *** No rule to make target `clean'. Stop. rm: Makefile: No such file or directory rm: CMakeLists.txt: No such file or directory rm: CMakeCache.txt: No such file or directory rm: CMakeFiles: No such file or directory rm: cmake_install.cmake: No such file or directory ./install: line 8: xmledit: command not found ./install: line 9: xml2cmake: command not found CMake Error: The source directory "/Users/shawley/apps/VizTools/CarpetHDF5" does not appear to contain CMakeLists.txt. Specify --help for usage, or press the help button on the CMake GUI. make: *** No targets specified and no makefile found. Stop.
On 4/10/12 3:24 PM, "Ian Hinder" ian.hinder@aei.mpg.de wrote:
On 10 Apr 2012, at 22:21, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Hi all. I'd like to visualise some 3D data produced by an initial-data run of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as recommended by cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the following error:
--
The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open
"/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol_c ou lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
--
I have no idea whether the file is corrupted, but wanted to know: is the CarpetHDF5 plugin up-to-date with the output of Maxwell's CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
One problem can come from Visit trying to open too many files for the maximum open file limit of your OS. Mac OS, for example, has a very small limit. Try changing this with ulimit. But ultimately, you should try to find the actual error message. I think there is an option for Visit to output the errors to a file, but it's so long since I've used Visit that I don't remember. Probably someone else can fill that in...
-- Ian Hinder http://numrel.aei.mpg.de/people/hinder
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Hi Scott,
the important errors are:
./install: line 8: xmledit: command not found ./install: line 9: xml2cmake: command not found
It appears that you need to set your PATH variable to your visit/bin directory.
I hope that helps. Christian
How did you get the plugin to compile? When I run the script I getŠ
~/apps/VizTools/CarpetHDF5] % ./install make: *** No rule to make target `clean'. Stop. rm: Makefile: No such file or directory rm: CMakeLists.txt: No such file or directory rm: CMakeCache.txt: No such file or directory rm: CMakeFiles: No such file or directory rm: cmake_install.cmake: No such file or directory ./install: line 8: xmledit: command not found ./install: line 9: xml2cmake: command not found CMake Error: The source directory "/Users/shawley/apps/VizTools/CarpetHDF5" does not appear to contain CMakeLists.txt. Specify --help for usage, or press the help button on the CMake GUI. make: *** No targets specified and no makefile found. Stop.
On 4/10/12 3:24 PM, "Ian Hinder" ian.hinder@aei.mpg.de wrote:
On 10 Apr 2012, at 22:21, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF
MARYLAND BALTIMORE COUNTY] wrote:
Hi all. I'd like to visualise some 3D data produced by an initial-data
run
of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as recommended
by
cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the
following error:
--
The metadata server running on host localhost has exited abnormally.
VisIt
is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open
"/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol_c ou
lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the
underlying
file format has changed and VisIt's readers have not been updated yet,
or
when the reader VisIt is using for your file format is not robust.
Please
check whether the file is corrupted and, if not, contact a VisIt
developer.
--
I have no idea whether the file is corrupted, but wanted to know: is the CarpetHDF5 plugin up-to-date with the output of Maxwell's CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
One problem can come from Visit trying to open too many files for the maximum open file limit of your OS. Mac OS, for example, has a very small limit. Try changing this with ulimit. But ultimately, you should try to find the actual error message. I think there is an option for Visit to output the errors to a file, but it's so long since I've used Visit that I don't remember. Probably someone else can fill that in...
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Is THAT where those are? I didn't see any instructions about that. I even tried downloading the xmledit plugin for vim... (http://www.vim.org/scripts/script.php?script_id=301)
This line should be changed: "To install the package, simply execute the install script contained in the CarpetHDF5 package."
to read
"To install the package, first set your path to include the Visin bin/ directory (e.g. /Applications/VisIt.app/Contents/Resources/bin/ or /usr/local/visit/bin/ ). Then run the install script contained in the CarpetHDF5 package."
Also... the instruction say "In the "Makefile"-tab modify the library and include path for the HDF5-library to match the installation on your system."
....there is no "Makefile" tab.
-Scott
On 4/12/12 2:32 PM, "Christian Reisswig" reisswig@tapir.caltech.edu wrote:
Hi Scott,
the important errors are:
./install: line 8: xmledit: command not found ./install: line 9: xml2cmake: command not found
It appears that you need to set your PATH variable to your visit/bin directory.
I hope that helps. Christian
How did you get the plugin to compile? When I run the script I getŠ
~/apps/VizTools/CarpetHDF5] % ./install make: *** No rule to make target `clean'. Stop. rm: Makefile: No such file or directory rm: CMakeLists.txt: No such file or directory rm: CMakeCache.txt: No such file or directory rm: CMakeFiles: No such file or directory rm: cmake_install.cmake: No such file or directory ./install: line 8: xmledit: command not found ./install: line 9: xml2cmake: command not found CMake Error: The source directory "/Users/shawley/apps/VizTools/CarpetHDF5" does not appear to contain CMakeLists.txt. Specify --help for usage, or press the help button on the CMake GUI. make: *** No targets specified and no makefile found. Stop.
On 4/10/12 3:24 PM, "Ian Hinder" ian.hinder@aei.mpg.de wrote:
On 10 Apr 2012, at 22:21, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF
MARYLAND BALTIMORE COUNTY] wrote:
Hi all. I'd like to visualise some 3D data produced by an
initial-data
run
of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as
recommended
by
cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the
following error:
--
The metadata server running on host localhost has exited abnormally.
VisIt
is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open
"/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol _c ou
lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the
underlying
file format has changed and VisIt's readers have not been updated
yet,
or
when the reader VisIt is using for your file format is not robust.
Please
check whether the file is corrupted and, if not, contact a VisIt
developer.
--
I have no idea whether the file is corrupted, but wanted to know: is
the
CarpetHDF5 plugin up-to-date with the output of Maxwell's
CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
One problem can come from Visit trying to open too many files for the maximum open file limit of your OS. Mac OS, for example, has a very small limit. Try changing this with ulimit. But ultimately, you
should
try to find the actual error message. I think there is an option for Visit to output the errors to a file, but it's so long since I've used Visit that I don't remember. Probably someone else can fill that in...
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Scott:
That tab is actually the second tab in the window that opens up. It's labelled "CMake" rather than "Makefile".
BTW, do you have "cmake" (rather than "make" or "gmake") installed on your system?
Bernard
---------------------------------------------------------------------------
Yes, I went to the cmake tab, changed the definitions, and generated code... I even changed the mpi lib to -L/sw/lib/openmpi
The error that then results is....
Running: xmledit2.4.2 CarpetHDF5.xml Running: xml2cmake2.4.2 CarpetHDF5.xml ----------------------------------------------------------------- Parsed document of type Plugin -----------------------------------------------------------------
Plugin: CarpetHDF5 ("Carpet AMR/curvilinear HDF5 output generated by the Cactus Computational Toolkit", type=database) -- version 2.1 Attribute: ()
-- The C compiler identification is GNU -- The CXX compiler identification is Clang -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Configuring done -- Generating done -- Build files have been written to: /Users/shawley/apps/VizTools/CarpetHDF5 Scanning dependencies of target ECarpetHDF5Database_par [ 6%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5EnginePluginInfo.C.o [ 12%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5PluginInfo.C.o [ 18%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5CommonPluginInfo.C.o [ 25%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/avtCarpetHDF5FileFormat.C.o [ 31%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/H5Index.C.o make[2]: *** No rule to make target `/usr/lib/libmpi_cxx.dylib', needed by `/Users/shawley/.visit/2.4.2/darwin-x86_64/plugins/databases/libECarpetHDF5 Database_par.dylib'. Stop. make[1]: *** [CMakeFiles/ECarpetHDF5Database_par.dir/all] Error 2
Not sure why it's looking for /usr/lib/libmpi_cxx.dylib when I told it to look elsewhere.
On 4/12/12 2:45 PM, "Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY]" bernard.j.kelly@nasa.gov wrote:
Scott:
That tab is actually the second tab in the window that opens up. It's labelled "CMake" rather than "Makefile".
BTW, do you have "cmake" (rather than "make" or "gmake") installed on your system?
Bernard
-- Bernard Kelly -- CRESST Research Associate, NASA/GSFC
Phone: +1 (301) 286-7243 E-Mail: bernard.j.kelly@nasa.gov Web: http://science.gsfc.nasa.gov/sed/index.cfm?fuseAction=people.jumpBio&iph... e bookid=13052
--
On 4/12/12 3:42 PM, "Scott Hawley" scott.hawley@belmont.edu wrote:
Is THAT where those are? I didn't see any instructions about that. I even tried downloading the xmledit plugin for vim... (http://www.vim.org/scripts/script.php?script_id=301)
This line should be changed: "To install the package, simply execute the install script contained in the CarpetHDF5 package."
to read
"To install the package, first set your path to include the Visin bin/ directory (e.g. /Applications/VisIt.app/Contents/Resources/bin/ or /usr/local/visit/bin/ ). Then run the install script contained in the CarpetHDF5 package."
Also... the instruction say "In the "Makefile"-tab modify the library and include path for the HDF5-library to match the installation on your system."
....there is no "Makefile" tab.
-Scott
On 4/12/12 2:32 PM, "Christian Reisswig" reisswig@tapir.caltech.edu wrote:
Hi Scott,
the important errors are:
./install: line 8: xmledit: command not found ./install: line 9: xml2cmake: command not found
It appears that you need to set your PATH variable to your visit/bin directory.
I hope that helps. Christian
How did you get the plugin to compile? When I run the script I getŠ
~/apps/VizTools/CarpetHDF5] % ./install make: *** No rule to make target `clean'. Stop. rm: Makefile: No such file or directory rm: CMakeLists.txt: No such file or directory rm: CMakeCache.txt: No such file or directory rm: CMakeFiles: No such file or directory rm: cmake_install.cmake: No such file or directory ./install: line 8: xmledit: command not found ./install: line 9: xml2cmake: command not found CMake Error: The source directory "/Users/shawley/apps/VizTools/CarpetHDF5" does not appear to contain CMakeLists.txt. Specify --help for usage, or press the help button on the CMake GUI. make: *** No targets specified and no makefile found. Stop.
On 4/10/12 3:24 PM, "Ian Hinder" ian.hinder@aei.mpg.de wrote:
On 10 Apr 2012, at 22:21, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY
OF
MARYLAND BALTIMORE COUNTY] wrote:
Hi all. I'd like to visualise some 3D data produced by an
initial-data
run
of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as
recommended
by
cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the
following error:
--
The metadata server running on host localhost has exited
abnormally.
VisIt
is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open
"/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahnd o l _c ou
lomb.h5". Each attempt to open it caused VisIt's metadata server
to
crash. This can occur when the file is corrupted, or when the
underlying
file format has changed and VisIt's readers have not been updated
yet,
or
when the reader VisIt is using for your file format is not robust.
Please
check whether the file is corrupted and, if not, contact a VisIt
developer.
--
I have no idea whether the file is corrupted, but wanted to know:
is the
CarpetHDF5 plugin up-to-date with the output of Maxwell's
CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
One problem can come from Visit trying to open too many files for the maximum open file limit of your OS. Mac OS, for example, has a very small limit. Try changing this with ulimit. But ultimately, you
should
try to find the actual error message. I think there is an option for Visit to output the errors to a file, but it's so long since I've
used
Visit that I don't remember. Probably someone else can fill that
in...
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Scott:
That tab is actually the second tab in the window that opens up. It's labelled "CMake" rather than "Makefile".
This was changed when they changed the build scripts from using from make to using cmake. I'll update the docs. Thanks for pointing this out! Christian
BTW, do you have "cmake" (rather than "make" or "gmake") installed on your system?
Bernard
Is THAT where those are? I didn't see any instructions about that. I even tried downloading the xmledit plugin for vim... (http://www.vim.org/scripts/script.php?script_id=301)
This line should be changed: "To install the package, simply execute the install script contained in the CarpetHDF5 package."
to read
"To install the package, first set your path to include the Visin bin/ directory (e.g. /Applications/VisIt.app/Contents/Resources/bin/ or /usr/local/visit/bin/ ). Then run the install script contained in the CarpetHDF5 package."
Also... the instruction say "In the "Makefile"-tab modify the library and include path for the HDF5-library to match the installation on your system."
....there is no "Makefile" tab.
-Scott
On 4/12/12 2:32 PM, "Christian Reisswig" reisswig@tapir.caltech.edu
wrote:
Hi Scott,
the important errors are:
./install: line 8: xmledit: command not found ./install: line 9: xml2cmake: command not found
It appears that you need to set your PATH variable to your visit/bin directory.
I hope that helps. Christian
How did you get the plugin to compile? When I run the script I getŠ
~/apps/VizTools/CarpetHDF5] % ./install make: *** No rule to make target `clean'. Stop. rm: Makefile: No such file or directory rm: CMakeLists.txt: No such file or directory rm: CMakeCache.txt: No such file or directory rm: CMakeFiles: No such file or directory rm: cmake_install.cmake: No such file or directory ./install: line 8: xmledit: command not found ./install: line 9: xml2cmake: command not found CMake Error: The source directory "/Users/shawley/apps/VizTools/CarpetHDF5" does not appear to contain CMakeLists.txt. Specify --help for usage, or press the help button on the CMake GUI. make: *** No targets specified and no makefile found. Stop.
On 4/10/12 3:24 PM, "Ian Hinder" ian.hinder@aei.mpg.de wrote:
On 10 Apr 2012, at 22:21, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF
MARYLAND BALTIMORE COUNTY] wrote:
Hi all. I'd like to visualise some 3D data produced by an
initial-data
run
of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as
recommended
by
cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the
following error:
--
--
The metadata server running on host localhost has exited abnormally.
VisIt
is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open
"/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndo l _c
ou
lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the
underlying
file format has changed and VisIt's readers have not been updated
yet,
or
when the reader VisIt is using for your file format is not robust.
Please
check whether the file is corrupted and, if not, contact a VisIt
developer.
--
--
I have no idea whether the file is corrupted, but wanted to know: is
the
CarpetHDF5 plugin up-to-date with the output of Maxwell's
CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
One problem can come from Visit trying to open too many files for the maximum open file limit of your OS. Mac OS, for example, has a very small limit. Try changing this with ulimit. But ultimately, you
should
try to find the actual error message. I think there is an option for Visit to output the errors to a file, but it's so long since I've used Visit that I don't remember. Probably someone else can fill that
in...
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Hi Bernard,
does h5ls work on that file? Are the permissions set correctly? The last time I tried the reader worked just fine (and this was two weeks ago).
cheers, Christian
Hi all. I'd like to visualise some 3D data produced by an initial-data run of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as recommended by cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the following error:
The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open "/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol_cou lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
I have no idea whether the file is corrupted, but wanted to know: is the CarpetHDF5 plugin up-to-date with the output of Maxwell's CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
Thanks,
Bernard
Beany, I use VisIt without problems with the Maxwell version of the Einstein Toolkit. Was your plugin compiled with the same HDF5 library version used to compile VisIt? Did you use h5ls to check the file is not corrupted?
Cheers, Bruno
On Apr 10, 2012, at 2:21 PM, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Hi all. I'd like to visualise some 3D data produced by an initial-data run of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as recommended by cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the following error:
The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open "/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol_cou lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer.
I have no idea whether the file is corrupted, but wanted to know: is the CarpetHDF5 plugin up-to-date with the output of Maxwell's CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
Thanks,
Bernard
-- Bernard Kelly -- CRESST Research Associate, NASA/GSFC
Phone: +1 (301) 286-7243 E-Mail: bernard.j.kelly@nasa.gov Web: http://science.gsfc.nasa.gov/sed/index.cfm?fuseAction=people.jumpBio&iph... bookid=13052
--
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Dr. Bruno Giacomazzo JILA - University of Colorado 440 UCB Boulder, CO 80309 USA
Tel. : +1 303-492-0389 Fax : +1 303-492-5235 email : bruno.giacomazzo@jila.colorado.edu web: http://www.brunogiacomazzo.org
---------------------------------------------------------------------- There are only 10 types of people in the world: Those who understand binary, and those who don't ----------------------------------------------------------------------
Hi Christian, Bruno, Roland.
h5ls seemed to indicate that the file wasn't corrupted )though perhaps I don't know what HDF5 corruption looks like):
----------------------------------------------------------------------------
h5ls hahndol::hahndol_coulomb.h5
HAHNDOL::Im_Coulomb\ it=0\ tl=0\ rl=0 Dataset {34, 61, 61} HAHNDOL::Re_Coulomb\ it=0\ tl=0\ rl=0 Dataset {34, 61, 61} Parameters\ and\ Global\ Attributes Group ----------------------------------------------------------------------------
Originally my Visit and plugins were compiled with slightly different versions of HDF5 (1.8.6 vs 1.8.7). I tried the HDF5_IGNORE_VERSION_CHECK variable, but it made no difference.
I've now moved to the 1.8.7 for both, but it doesn't help (apart from removing warnings about HDF5_IGNORE_VERSION_CHECK). The terminal output from Visit is:
--------------------------------------------------- Running: gui2.4.2 Running: viewer2.4.2 -host 127.0.0.1 -port 5600 -geometry 875x778+405+0 -borders 20,0,0,1 -shift 0,0 -preshift 0,0 -defer Running: mdserver2.4.2 -host 127.0.0.1 -port 5601 mdserver(17278) malloc: *** error for object 0x7fff70bc2500: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug Running: mdserver2.4.2 -host 127.0.0.1 -port 5601 mdserver(17341) malloc: *** error for object 0x7fff70bc2500: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug Running: mdserver2.4.2 -host 127.0.0.1 -port 5601 mdserver(17362) malloc: *** error for object 0x7fff70bc2500: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug Running: mdserver2.4.2 -host 127.0.0.1 -port 5600 mdserver(17383) malloc: *** error for object 0x7fff70bc2500: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug Running: mdserver2.4.2 -host 127.0.0.1 -port 5600 ---------------------------------------------------
I'm not sure it's not my Visit installation itself. I got the pre-compiled Mac package. I'm trying a from-source installation instead, but am briefly hung up getting the pre-requisite VTK on my machine.
Thanks,
Bernard
----------------------------------------------------------------------------- Bernard Kelly -- CRESST Research Associate, NASA/GSFC
Phone: +1 (301) 286-7243 E-Mail: bernard.j.kelly@nasa.gov Web: http://science.gsfc.nasa.gov/sed/index.cfm?fuseAction=people.jumpBio&iph... -----------------------------------------------------------------------------
From: Bruno Giacomazzo <bruno.giacomazzo@jila.colorado.edumailto:bruno.giacomazzo@jila.colorado.edu> Date: Tue, 10 Apr 2012 15:27:39 -0500 To: Bernard Kelly <bernard.j.kelly@nasa.govmailto:bernard.j.kelly@nasa.gov> Cc: Einstein Toolkit Users <users@einsteintoolkit.orgmailto:users@einsteintoolkit.org> Subject: Re: [Users] Visit & CarpetHDF5 mismatch?
Beany, I use VisIt without problems with the Maxwell version of the Einstein Toolkit. Was your plugin compiled with the same HDF5 library version used to compile VisIt? Did you use h5ls to check the file is not corrupted?
Cheers, Bruno
On Apr 10, 2012, at 2:21 PM, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
Hi all. I'd like to visualise some 3D data produced by an initial-data run of the EinsteinToolkit (Maxwell).
I'm outputting using CarpetIOHDF5; I have an output file "hahndol::hahndol_coulomb.h5", and decided to use Visit, as recommended by cactuscode, etc.
I grabbed the CarpetHDF5 plugin code from svn, and installed as per instructions (pointing at the ETK-installed HDF5 in my Cactus/configs/<config-name>/scratch/external directory).
Starting Visit (2.4.2) , and trying to load a .h5 file yields the following error:
--------------------------------------------------------------------------- ---- The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open "/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol_cou lomb.h5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer. --------------------------------------------------------------------------- ----
I have no idea whether the file is corrupted, but wanted to know: is the CarpetHDF5 plugin up-to-date with the output of Maxwell's CarpetIOHDF5?
Any basic ideas where I might have gone wrong?
Thanks,
Bernard
--------------------------------------------------------------------------- -- Bernard Kelly -- CRESST Research Associate, NASA/GSFC
Phone: +1 (301) 286-7243 E-Mail: bernard.j.kelly@nasa.govmailto:bernard.j.kelly@nasa.gov Web: http://science.gsfc.nasa.gov/sed/index.cfm?fuseAction=people.jumpBio&iph... bookid=13052 --------------------------------------------------------------------------- --
_______________________________________________ Users mailing list Users@einsteintoolkit.orgmailto:Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Dr. Bruno Giacomazzo JILA - University of Colorado 440 UCB Boulder, CO 80309 USA
Tel. : +1 303-492-0389 Fax : +1 303-492-5235 email : bruno.giacomazzo@jila.colorado.edumailto:bruno.giacomazzo@jila.colorado.edu web: http://www.brunogiacomazzo.org
---------------------------------------------------------------------- There are only 10 types of people in the world: Those who understand binary, and those who don't ----------------------------------------------------------------------
users@lists.einsteintoolkit.org
-
Bruno Giacomazzo -
Christian Reisswig -
Erik Schnetter -
Ian Hinder -
Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] -
Roland Haas -
Scott Hawley