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SeismicData / asdf-library

Adaptable Seismic Data Format
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specfem3d_globe output to asdf very slow #16

Open lermert opened 8 years ago

lermert commented 8 years ago

Hej there, I am trying to output specfem 3D globe synthetics in large number, like 100 000 seismograms per component. Writing these to binary sac in parallel is very fast, (for a short, very low frequency test setup about 10 minutes) but the handling of the data becomes extremely cumbersome. Thus, asdf would be perfect for my purposes.

I am running specfem3D_globe on Piz Daint (http://www.cscs.ch/computers/piz_daint_piz_dora/index.html), we managed to compile specfem with asdf, but when running the model with my 100000 receivers the writing stalled. I could watch the size of the synthetics.h5 go up megabyte by megabyte. After two hours I cancelled the job (of which the actual calculation takes a couple of minutes at most). I append the compilation file, Parameters and solver output. I had it write after 1000 time steps, that's why the output stops there. Maybe you can look into this, it would be great if you have an idea what's causing the trouble :) cheers

mk_daint.txt output_solver.asdf.txt Par_file.asdf.txt

ghost commented 8 years ago

Thanks for reporting. Can you send me the STATIONS file also? I will test it on our cluster and see if I can figure out why it is so slow for this number of receivers.

lermert commented 8 years ago

yep! Here it is. Thanks :)

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

On 24 Nov 2015, at 20:18, James Smith notifications@github.com<mailto:notifications@github.com> wrote:

Thanks for reporting. Can you send me the STATIONS file also? I will test it on our cluster and see if I can figure out why it is so slow for this number of receivers.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-159378016.

ghost commented 8 years ago

Sorry but can you send it again? I don't see the STATIONS file

Also, are you using the development version from CIG? If that's the case, then your example won't work as I know output is broken if number of time steps < NSTEP_BETWEEN_OUTPUT_SEISMOS (based on your Par_file settings) for that version.

The development verison on my repository fixes this issue (and quite a few other issues with the ASDF writer). It will be pushed to the CIG repository this week after I receive feedback from another user.

But if I can get the STATIONS file I can test the version from my repository to make sure it works and has acceptable performance as I haven't run an example with that number of stations before.

Thanks.

lermert commented 8 years ago

hmm, yes, I am using the devel branch from github. However, my nr. of time steps in total (1200) is > than nstep between output seismos (1000). I append the stations file again with .txt appended, sometimes our mail server blocks stuff if the extension looks suspicious, so maybe it doesn’t like to extension at all. cheers :)

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 24 Nov 2015, at 20:32, James Smith notifications@github.com<mailto:notifications@github.com> wrote:

Sorry but can you send it again? I don't see the STATIONS file

Also, are you using the development version from CIG? If that's the case, then your example won't work as I know output is broken if number of time steps < NSTEP_BETWEEN_OUTPUT_SEISMOS (based on your Par_file settings) for that version.

The development verison on my repository fixes this issue (and quite a few other issues with the ASDF writer). It will be pushed to the CIG repository this week after I receive feedback from another user.

But if I can get the STATIONS file I can test the version from my repository to make sure it works and has acceptable performance as I haven't run an example with that number of stations before.

Thanks.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-159381567.

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ghost commented 8 years ago

Ah, yes I meant that nstep between output seismos < total then it won't work with the devel branch from github (unless you use my branch). I will test your example later today and see how it goes. Thanks.

ghost commented 8 years ago

Also that STATIONS file you pasted cut off after 1565 Stations. I can just make my own file with a script so I'll just do that.

lermert commented 8 years ago

Hi hi, I just tried writing everything only at the end, just to make sure that wasn’t the problem, but it’s still writing very slowly. Thanks in advance, anyway. I appreciate any suggestion.

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 24 Nov 2015, at 20:42, James Smith notifications@github.com<mailto:notifications@github.com> wrote:

Ah, yes I meant that nstep between output seismos < total then it won't work with the devel branch from github (unless you use my branch). I will test your example later today and see how it goes. Thanks.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-159384170.

ghost commented 8 years ago

A quick update.

I ran specfem3d_globe for 25000 stations using ASDF writer and it completed in 3 minutes and 12 seconds (traces were 0.5 minutes versus 2 minutes in your case). ASDF output looks fine in ObsPy. When I attempt >30000 stations, I run into memory exceeded issues on my cluster (I'm using 8 GB/node--should be plenty). Again thanks for pointing this out. It seems there is a problem with the ASDF writer using too much memory for this number of stations.

When I use SAC binary, the solver works fine so this is something I should fix.

lermert commented 8 years ago

Hi James!

Happy new year! I wanted to follow up on the question of writing ~50000 seismograms from specfem3Dglobe to ASDF file…I think Lion said that this issue was fixed. Now I was wondering what I need to reinstall to make it work on the cluster here. Just pull the newest specfem development branch?

Best, Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 25 Nov 2015, at 00:22, James Smith notifications@github.com<mailto:notifications@github.com> wrote:

A quick update.

I ran specfem3d_globe for 25000 stations using ASDF writer and it completed in 3 minutes and 12 seconds (traces were 0.5 minutes versus 2 minutes in your case). ASDF output looks fine in ObsPy. When I attempt >30000 stations, I run into memory exceeded issues on my cluster (I'm using 8 GB/node--should be plenty). Again thanks for pointing this out. It seems there is a problem with the ASDF writer using too much memory for this number of stations.

When I use SAC binary, the solver works fine so this is something I should fix.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-159437346.

ghost commented 8 years ago

Hi Laura,

Thanks! It's too early to say that this issue is fixed, but I now get reasonable performance on 384 cores on ~6000 seismograms for 60 minute duration. I'm going to push my changes in the next day or so and I'll update you when I do. I need to test on a larger number of receivers and a larger number of cores.

Cheers, James

From: lermert [notifications@github.com] Sent: Monday, January 04, 2016 9:55 AM To: SeismicData/asdf-library Cc: James A. Smith Subject: Re: [asdf-library] specfem3d_globe output to asdf very slow (#16)

Hi James!

Happy new year! I wanted to follow up on the question of writing ~50000 seismograms from specfem3Dglobe to ASDF file…I think Lion said that this issue was fixed. Now I was wondering what I need to reinstall to make it work on the cluster here. Just pull the newest specfem development branch?

Best, Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 25 Nov 2015, at 00:22, James Smith notifications@github.com<mailto:notifications@github.com> wrote:

A quick update.

I ran specfem3d_globe for 25000 stations using ASDF writer and it completed in 3 minutes and 12 seconds (traces were 0.5 minutes versus 2 minutes in your case). ASDF output looks fine in ObsPy. When I attempt >30000 stations, I run into memory exceeded issues on my cluster (I'm using 8 GB/node--should be plenty). Again thanks for pointing this out. It seems there is a problem with the ASDF writer using too much memory for this number of stations.

When I use SAC binary, the solver works fine so this is something I should fix.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-159437346.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-168714369.

ghost commented 8 years ago

Hi Laura,

I’ve uploaded a newer asdf-lib with the latest library fix. There is still heavy memory usage when I tasted it, so it may not work for your case yet. If you have time to try it, let me know if there are any improvements. I’ll continue working on this as time permits.

Cheers, James

On Jan 4, 2016, at 10:55 AM, lermert notifications@github.com<mailto:notifications@github.com> wrote:

Hi James!

Happy new year! I wanted to follow up on the question of writing ~50000 seismograms from specfem3Dglobe to ASDF file…I think Lion said that this issue was fixed. Now I was wondering what I need to reinstall to make it work on the cluster here. Just pull the newest specfem development branch?

Best, Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 25 Nov 2015, at 00:22, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

A quick update.

I ran specfem3d_globe for 25000 stations using ASDF writer and it completed in 3 minutes and 12 seconds (traces were 0.5 minutes versus 2 minutes in your case). ASDF output looks fine in ObsPy. When I attempt >30000 stations, I run into memory exceeded issues on my cluster (I'm using 8 GB/node--should be plenty). Again thanks for pointing this out. It seems there is a problem with the ASDF writer using too much memory for this number of stations.

When I use SAC binary, the solver works fine so this is something I should fix.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-159437346.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-168714369.

lermert commented 8 years ago

Hi James,

I have a short question…I have trouble compiling with ADIOS support; is that needed for ASDF? Otherwise I’ll be easier off without.

Also, our compiler here keeps complaining about the -Wl flag in this line:

SPECFEM_LINK_FLAGS += $(ASDF_LIBS) -lhdf5hl_fortran -lhdf5_hl -lhdf5 -Wl -lstdc++

In the src/specfem3D/rules.mk, so I removed this flag; not sure if that is a problem.

Thanks and best,

Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 05 Jan 2016, at 23:06, James Smith notifications@github.com<mailto:notifications@github.com> wrote:

Hi Laura,

I’ve uploaded a newer asdf-lib with the latest library fix. There is still heavy memory usage when I tasted it, so it may not work for your case yet. If you have time to try it, let me know if there are any improvements. I’ll continue working on this as time permits.

Cheers, James

On Jan 4, 2016, at 10:55 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Hi James!

Happy new year! I wanted to follow up on the question of writing ~50000 seismograms from specfem3Dglobe to ASDF file…I think Lion said that this issue was fixed. Now I was wondering what I need to reinstall to make it work on the cluster here. Just pull the newest specfem development branch?

Best, Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 25 Nov 2015, at 00:22, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

A quick update.

I ran specfem3d_globe for 25000 stations using ASDF writer and it completed in 3 minutes and 12 seconds (traces were 0.5 minutes versus 2 minutes in your case). ASDF output looks fine in ObsPy. When I attempt >30000 stations, I run into memory exceeded issues on my cluster (I'm using 8 GB/node--should be plenty). Again thanks for pointing this out. It seems there is a problem with the ASDF writer using too much memory for this number of stations.

When I use SAC binary, the solver works fine so this is something I should fix.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-159437346.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-168714369.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169148951.

ghost commented 8 years ago

Hi Laura,

ADIOS isn’t need for ASDF.

The -WI option should be for warnings that violate fortran. I didn’t get any problems on my end. I’m using intel-13.1 for compiling, so maybe there’s a problem with other compilers.

Thanks for letting me know, James

On Jan 6, 2016, at 11:31 AM, lermert notifications@github.com<mailto:notifications@github.com> wrote:

Hi James,

I have a short question…I have trouble compiling with ADIOS support; is that needed for ASDF? Otherwise I’ll be easier off without.

Also, our compiler here keeps complaining about the -Wl flag in this line:

SPECFEM_LINK_FLAGS += $(ASDF_LIBS) -lhdf5hl_fortran -lhdf5_hl -lhdf5 -Wl -lstdc++

In the src/specfem3D/rules.mk, so I removed this flag; not sure if that is a problem.

Thanks and best,

Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 05 Jan 2016, at 23:06, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Laura,

I’ve uploaded a newer asdf-lib with the latest library fix. There is still heavy memory usage when I tasted it, so it may not work for your case yet. If you have time to try it, let me know if there are any improvements. I’ll continue working on this as time permits.

Cheers, James

On Jan 4, 2016, at 10:55 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi James!

Happy new year! I wanted to follow up on the question of writing ~50000 seismograms from specfem3Dglobe to ASDF file…I think Lion said that this issue was fixed. Now I was wondering what I need to reinstall to make it work on the cluster here. Just pull the newest specfem development branch?

Best, Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 25 Nov 2015, at 00:22, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

A quick update.

I ran specfem3d_globe for 25000 stations using ASDF writer and it completed in 3 minutes and 12 seconds (traces were 0.5 minutes versus 2 minutes in your case). ASDF output looks fine in ObsPy. When I attempt >30000 stations, I run into memory exceeded issues on my cluster (I'm using 8 GB/node--should be plenty). Again thanks for pointing this out. It seems there is a problem with the ASDF writer using too much memory for this number of stations.

When I use SAC binary, the solver works fine so this is something I should fix.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-159437346.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-168714369.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169148951.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169380148.

ghost commented 8 years ago

Also, please update the asdf-lib to the latest version before testing the ASDF writer. I added a fix yesterday for the library.

On Jan 6, 2016, at 11:40 AM, James A. Smith jas11@exchange.Princeton.EDU<mailto:jas11@exchange.princeton.edu> wrote:

Hi Laura,

ADIOS isn’t need for ASDF.

The -WI option should be for warnings that violate fortran. I didn’t get any problems on my end. I’m using intel-13.1 for compiling, so maybe there’s a problem with other compilers.

Thanks for letting me know, James

On Jan 6, 2016, at 11:31 AM, lermert notifications@github.com<mailto:notifications@github.com> wrote:

Hi James,

I have a short question…I have trouble compiling with ADIOS support; is that needed for ASDF? Otherwise I’ll be easier off without.

Also, our compiler here keeps complaining about the -Wl flag in this line:

SPECFEM_LINK_FLAGS += $(ASDF_LIBS) -lhdf5hl_fortran -lhdf5_hl -lhdf5 -Wl -lstdc++

In the src/specfem3D/rules.mk, so I removed this flag; not sure if that is a problem.

Thanks and best,

Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 05 Jan 2016, at 23:06, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Laura,

I’ve uploaded a newer asdf-lib with the latest library fix. There is still heavy memory usage when I tasted it, so it may not work for your case yet. If you have time to try it, let me know if there are any improvements. I’ll continue working on this as time permits.

Cheers, James

On Jan 4, 2016, at 10:55 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi James!

Happy new year! I wanted to follow up on the question of writing ~50000 seismograms from specfem3Dglobe to ASDF file…I think Lion said that this issue was fixed. Now I was wondering what I need to reinstall to make it work on the cluster here. Just pull the newest specfem development branch?

Best, Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 25 Nov 2015, at 00:22, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

A quick update.

I ran specfem3d_globe for 25000 stations using ASDF writer and it completed in 3 minutes and 12 seconds (traces were 0.5 minutes versus 2 minutes in your case). ASDF output looks fine in ObsPy. When I attempt >30000 stations, I run into memory exceeded issues on my cluster (I'm using 8 GB/node--should be plenty). Again thanks for pointing this out. It seems there is a problem with the ASDF writer using too much memory for this number of stations.

When I use SAC binary, the solver works fine so this is something I should fix.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-159437346.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-168714369.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169148951.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169380148.

lermert commented 8 years ago

Hi Hi James!

It took me a while to recompile everything — had to remember how to do that, which should be faster now in the future. Unfortunately when I ran it on a 20-minute seismogram test, I received a bunch of error messages: The synthetics.h5 file is opened, but then the waveforms not successfully written, although the station names are successfully included. Let me know if I can change something to make it work. Cheers! Laura

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2HDF5-DIAG: Error detected in HDF5 (1.8.14) : MPI-process 1 #000: H5D.c line 165 in H5Dcreate2(): not a location ID : major: Invalid arguments to routine minor: Inappropriate type

000: H5D.c line 165 in H5Dcreate2(): not a location ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine
major: Invalid arguments to routine
minor: Inappropriate type
minor: Bad value

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine
minor: Bad value

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0HDF5-DIAG: Error detected in HDF5 (1.8.14) : HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2MPI-process 1:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

major: Invalid arguments to routine

000: H5D.c line 165 in H5Dcreate2(): not a location ID

minor: Inappropriate type
major: Invalid arguments to routine
major: Invalid arguments to routine
minor: Inappropriate type
minor: Inappropriate type

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

minor: Bad value
major: Invalid arguments to routine
major: Invalid arguments to routine
minor: Bad value
minor: Bad value

….. Etc, etc, etc ….

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine
minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine
minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine
minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5F.c line 795 in H5Fclose(): decrementing file ID failed

major: Object atom
minor: Unable to close file

001: H5I.c line 1475 in H5I_dec_app_ref(): can't decrement ID ref count

major: Object atom
minor: Unable to decrement reference count

002: H5Fint.c line 1251 in H5F_close(): can't close file, there are objects still open

major: File accessibilty

minor: Unable to close file

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

ghost commented 8 years ago

Hi Laura,

It looks like my merge of the original_ASDF branch that has the working writer to the devel branch on github didn’t work. Sorry about that.

It looks like the old writer is still on the devel branch. I will fix it later today and update you.

Cheers, James

On Jan 7, 2016, at 11:22 AM, lermert notifications@github.com<mailto:notifications@github.com> wrote:

Hi Hi James!

It took me a while to recompile everything — had to remember how to do that, which should be faster now in the future. Unfortunately when I ran it on a 20-minute seismogram test, I received a bunch of error messages: The synthetics.h5 file is opened, but then the waveforms not successfully written, although the station names are successfully included. Let me know if I can change something to make it work. Cheers! Laura

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2HDF5-DIAG: Error detected in HDF5 (1.8.14) : MPI-process 1 #000: H5D.c line 165 in H5Dcreate2(): not a location ID : major: Invalid arguments to routine minor: Inappropriate type

000: H5D.c line 165 in H5Dcreate2(): not a location ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Bad value

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0HDF5-DIAG: Error detected in HDF5 (1.8.14) : HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2MPI-process 1:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

major: Invalid arguments to routine

000: H5D.c line 165 in H5Dcreate2(): not a location ID

minor: Inappropriate type major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Inappropriate type

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

minor: Bad value major: Invalid arguments to routine major: Invalid arguments to routine minor: Bad value minor: Bad value

….. Etc, etc, etc ….

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5F.c line 795 in H5Fclose(): decrementing file ID failed

major: Object atom minor: Unable to close file

001: H5I.c line 1475 in H5I_dec_app_ref(): can't decrement ID ref count

major: Object atom minor: Unable to decrement reference count

002: H5Fint.c line 1251 in H5F_close(): can't close file, there are objects still open

major: File accessibilty

minor: Unable to close file

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169714255.

lermert commented 8 years ago

No problem! Thanks a lot :) (at least I know again how to compile, haha)

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 07 Jan 2016, at 18:51, James Smith notifications@github.com<mailto:notifications@github.com> wrote:

Hi Laura,

It looks like my merge of the original_ASDF branch that has the working writer to the devel branch on github didn’t work. Sorry about that.

It looks like the old writer is still on the devel branch. I will fix it later today and update you.

Cheers, James

On Jan 7, 2016, at 11:22 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Hi James!

It took me a while to recompile everything — had to remember how to do that, which should be faster now in the future. Unfortunately when I ran it on a 20-minute seismogram test, I received a bunch of error messages: The synthetics.h5 file is opened, but then the waveforms not successfully written, although the station names are successfully included. Let me know if I can change something to make it work. Cheers! Laura

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2HDF5-DIAG: Error detected in HDF5 (1.8.14) : MPI-process 1 #000: H5D.c line 165 in H5Dcreate2(): not a location ID : major: Invalid arguments to routine minor: Inappropriate type

000: H5D.c line 165 in H5Dcreate2(): not a location ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Bad value

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0HDF5-DIAG: Error detected in HDF5 (1.8.14) : HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2MPI-process 1:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

major: Invalid arguments to routine

000: H5D.c line 165 in H5Dcreate2(): not a location ID

minor: Inappropriate type major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Inappropriate type

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

minor: Bad value major: Invalid arguments to routine major: Invalid arguments to routine minor: Bad value minor: Bad value

….. Etc, etc, etc ….

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5F.c line 795 in H5Fclose(): decrementing file ID failed

major: Object atom minor: Unable to close file

001: H5I.c line 1475 in H5I_dec_app_ref(): can't decrement ID ref count

major: Object atom minor: Unable to decrement reference count

002: H5Fint.c line 1251 in H5F_close(): can't close file, there are objects still open

major: File accessibilty

minor: Unable to close file

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169714255.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169755077.

ghost commented 8 years ago

Can you try again? Also, please double check you compiled and linked to the latest asdf-lib.

Thanks, James

On Jan 7, 2016, at 12:55 PM, lermert notifications@github.com<mailto:notifications@github.com> wrote:

No problem! Thanks a lot :) (at least I know again how to compile, haha)

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 07 Jan 2016, at 18:51, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Laura,

It looks like my merge of the original_ASDF branch that has the working writer to the devel branch on github didn’t work. Sorry about that.

It looks like the old writer is still on the devel branch. I will fix it later today and update you.

Cheers, James

On Jan 7, 2016, at 11:22 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Hi James!

It took me a while to recompile everything — had to remember how to do that, which should be faster now in the future. Unfortunately when I ran it on a 20-minute seismogram test, I received a bunch of error messages: The synthetics.h5 file is opened, but then the waveforms not successfully written, although the station names are successfully included. Let me know if I can change something to make it work. Cheers! Laura

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2HDF5-DIAG: Error detected in HDF5 (1.8.14) : MPI-process 1 #000: H5D.c line 165 in H5Dcreate2(): not a location ID : major: Invalid arguments to routine minor: Inappropriate type

000: H5D.c line 165 in H5Dcreate2(): not a location ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Bad value

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0HDF5-DIAG: Error detected in HDF5 (1.8.14) : HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2MPI-process 1:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

major: Invalid arguments to routine

000: H5D.c line 165 in H5Dcreate2(): not a location ID

minor: Inappropriate type major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Inappropriate type

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

minor: Bad value major: Invalid arguments to routine major: Invalid arguments to routine minor: Bad value minor: Bad value

….. Etc, etc, etc ….

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5F.c line 795 in H5Fclose(): decrementing file ID failed

major: Object atom minor: Unable to close file

001: H5I.c line 1475 in H5I_dec_app_ref(): can't decrement ID ref count

major: Object atom minor: Unable to decrement reference count

002: H5Fint.c line 1251 in H5F_close(): can't close file, there are objects still open

major: File accessibilty

minor: Unable to close file

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169714255.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169755077.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169756157.

lermert commented 8 years ago

Hi James!

Just to be sure I get the right one, I am cloning the master branch on https://github.com/SeismicData/asdf-library...correct me if I need another branch. I'll try again first thing tomorrow! Best Laura

Institut f�r Geophysik, ETH Z�rich Laura Ermert (PhD student) NO H 52.2 8092 Z�rich Schweiz

From: James Smith [notifications@github.com] Sent: Thursday, January 07, 2016 8:13 PM To: SeismicData/asdf-library Cc: Ermert Laura Subject: Re: [asdf-library] specfem3d_globe output to asdf very slow (#16)

Can you try again? Also, please double check you compiled and linked to the latest asdf-lib.

Thanks, James

On Jan 7, 2016, at 12:55 PM, lermert notifications@github.com<mailto:notifications@github.com> wrote:

No problem! Thanks a lot :) (at least I know again how to compile, haha)

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

On 07 Jan 2016, at 18:51, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Laura,

It looks like my merge of the original_ASDF branch that has the working writer to the devel branch on github didn�t work. Sorry about that.

It looks like the old writer is still on the devel branch. I will fix it later today and update you.

Cheers, James

On Jan 7, 2016, at 11:22 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Hi James!

It took me a while to recompile everything � had to remember how to do that, which should be faster now in the future. Unfortunately when I ran it on a 20-minute seismogram test, I received a bunch of error messages: The synthetics.h5 file is opened, but then the waveforms not successfully written, although the station names are successfully included. Let me know if I can change something to make it work. Cheers! Laura

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2HDF5-DIAG: Error detected in HDF5 (1.8.14) : MPI-process 1 #000: H5D.c line 165 in H5Dcreate2(): not a location ID : major: Invalid arguments to routine minor: Inappropriate type

000: H5D.c line 165 in H5Dcreate2(): not a location ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Bad value

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0HDF5-DIAG: Error detected in HDF5 (1.8.14) : HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2MPI-process 1:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

major: Invalid arguments to routine

000: H5D.c line 165 in H5Dcreate2(): not a location ID

minor: Inappropriate type major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Inappropriate type

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

minor: Bad value major: Invalid arguments to routine major: Invalid arguments to routine minor: Bad value minor: Bad value

�.. Etc, etc, etc �.

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5F.c line 795 in H5Fclose(): decrementing file ID failed

major: Object atom minor: Unable to close file

001: H5I.c line 1475 in H5I_dec_app_ref(): can't decrement ID ref count

major: Object atom minor: Unable to decrement reference count

002: H5Fint.c line 1251 in H5F_close(): can't close file, there are objects still open

major: File accessibilty

minor: Unable to close file

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169714255.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169755077.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169756157.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169777531.

lermert commented 8 years ago

Hi James!

Just to be sure I get the right one, I am cloning the master branch on https://github.com/SeismicData/asdf-library...just correct me if I need another branch. I'll try again first thing tomorrow morning! Best Laura

Institut f�r Geophysik, ETH Z�rich Laura Ermert (PhD student) NO H 52.2 8092 Z�rich Schweiz

From: James Smith [notifications@github.com] Sent: Thursday, January 07, 2016 8:13 PM To: SeismicData/asdf-library Cc: Ermert Laura Subject: Re: [asdf-library] specfem3d_globe output to asdf very slow (#16)

Can you try again? Also, please double check you compiled and linked to the latest asdf-lib.

Thanks, James

On Jan 7, 2016, at 12:55 PM, lermert notifications@github.com<mailto:notifications@github.com> wrote:

No problem! Thanks a lot :) (at least I know again how to compile, haha)

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

On 07 Jan 2016, at 18:51, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Laura,

It looks like my merge of the original_ASDF branch that has the working writer to the devel branch on github didn�t work. Sorry about that.

It looks like the old writer is still on the devel branch. I will fix it later today and update you.

Cheers, James

On Jan 7, 2016, at 11:22 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Hi James!

It took me a while to recompile everything � had to remember how to do that, which should be faster now in the future. Unfortunately when I ran it on a 20-minute seismogram test, I received a bunch of error messages: The synthetics.h5 file is opened, but then the waveforms not successfully written, although the station names are successfully included. Let me know if I can change something to make it work. Cheers! Laura

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2HDF5-DIAG: Error detected in HDF5 (1.8.14) : MPI-process 1 #000: H5D.c line 165 in H5Dcreate2(): not a location ID : major: Invalid arguments to routine minor: Inappropriate type

000: H5D.c line 165 in H5Dcreate2(): not a location ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Bad value

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0HDF5-DIAG: Error detected in HDF5 (1.8.14) : HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2MPI-process 1:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

major: Invalid arguments to routine

000: H5D.c line 165 in H5Dcreate2(): not a location ID

minor: Inappropriate type major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Inappropriate type

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

minor: Bad value major: Invalid arguments to routine major: Invalid arguments to routine minor: Bad value minor: Bad value

�.. Etc, etc, etc �.

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5F.c line 795 in H5Fclose(): decrementing file ID failed

major: Object atom minor: Unable to close file

001: H5I.c line 1475 in H5I_dec_app_ref(): can't decrement ID ref count

major: Object atom minor: Unable to decrement reference count

002: H5Fint.c line 1251 in H5F_close(): can't close file, there are objects still open

major: File accessibilty

minor: Unable to close file

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169714255.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169755077.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169756157.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169777531.

ghost commented 8 years ago

Yup, it’s the master branch. Sounds good!

On Jan 7, 2016, at 4:56 PM, lermert notifications@github.com<mailto:notifications@github.com> wrote:

Hi James!

Just to be sure I get the right one, I am cloning the master branch on https://github.com/SeismicData/asdf-library...just correct me if I need another branch. I'll try again first thing tomorrow morning! Best Laura

Institut f�r Geophysik, ETH Z�rich Laura Ermert (PhD student) NO H 52.2 8092 Z�rich Schweiz

From: James Smith [notifications@github.commailto:notifications@github.com] Sent: Thursday, January 07, 2016 8:13 PM To: SeismicData/asdf-library Cc: Ermert Laura Subject: Re: [asdf-library] specfem3d_globe output to asdf very slow (#16)

Can you try again? Also, please double check you compiled and linked to the latest asdf-lib.

Thanks, James

On Jan 7, 2016, at 12:55 PM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

No problem! Thanks a lot :) (at least I know again how to compile, haha)

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

On 07 Jan 2016, at 18:51, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Laura,

It looks like my merge of the original_ASDF branch that has the working writer to the devel branch on github didn�t work. Sorry about that.

It looks like the old writer is still on the devel branch. I will fix it later today and update you.

Cheers, James

On Jan 7, 2016, at 11:22 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Hi James!

It took me a while to recompile everything � had to remember how to do that, which should be faster now in the future. Unfortunately when I ran it on a 20-minute seismogram test, I received a bunch of error messages: The synthetics.h5 file is opened, but then the waveforms not successfully written, although the station names are successfully included. Let me know if I can change something to make it work. Cheers! Laura

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2HDF5-DIAG: Error detected in HDF5 (1.8.14) : MPI-process 1 #000: H5D.c line 165 in H5Dcreate2(): not a location ID : major: Invalid arguments to routine minor: Inappropriate type

000: H5D.c line 165 in H5Dcreate2(): not a location ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Bad value

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0HDF5-DIAG: Error detected in HDF5 (1.8.14) : HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2MPI-process 1:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

major: Invalid arguments to routine

000: H5D.c line 165 in H5Dcreate2(): not a location ID

minor: Inappropriate type major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Inappropriate type

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

minor: Bad value major: Invalid arguments to routine major: Invalid arguments to routine minor: Bad value minor: Bad value

�.. Etc, etc, etc �.

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5F.c line 795 in H5Fclose(): decrementing file ID failed

major: Object atom minor: Unable to close file

001: H5I.c line 1475 in H5I_dec_app_ref(): can't decrement ID ref count

major: Object atom minor: Unable to decrement reference count

002: H5Fint.c line 1251 in H5F_close(): can't close file, there are objects still open

major: File accessibilty

minor: Unable to close file

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169714255.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169755077.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169756157.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169777531.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169818791.

lermert commented 8 years ago

Hi James,

unfortunately, still the same. I used the master branch at asdf-library, deleted my old executable, compiled, linked against this one during specfem compilation, compiled specfem, but no change.

Do you think it could be related to the settings I use for compilation? I pasted the module list below, the last few are the ones I loaded for compiling asdf. cheers from over here, Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

1) modules/3.2.10.3 2) eswrap/1.1.0-1.020200.1231.0 3) switch/1.0-1.0502.60522.1.61.ari 4) craype-network-aries 5) gcc/4.8.2 6) craype/2.4.0 7) craype-sandybridge 8) slurm 9) cray-mpich/7.2.2 10) alps/5.2.4-2.0502.9822.32.1.ari 11) ddt/5.1 12) cudatoolkit/6.5.14-1.0502.9836.8.1 13) totalview-support/1.1.4 14) totalview/8.11.0 15) cray-libsci/13.0.4 16) udreg/2.3.2-1.0502.10518.2.17.ari 17) ugni/6.0-1.0502.10863.8.29.ari 18) pmi/5.0.7-1.0000.10678.155.25.ari 19) dmapp/7.0.1-1.0502.11080.8.76.ari 20) gni-headers/4.0-1.0502.10859.7.8.ari 21) xpmem/0.1-2.0502.64982.5.3.ari 22) dvs/2.5_0.9.0-1.0502.2188.1.116.ari 23) alps/5.2.4-2.0502.9774.31.11.ari 24) rca/1.0.0-2.0502.60530.1.62.ari 25) atp/1.8.2 26) PrgEnv-gnu/5.2.82 27) cmake/3.3.2 28) cray-hdf5-parallel/1.8.14 29) boost/1.58.0

On 07 Jan 2016, at 23:13, James Smith notifications@github.com<mailto:notifications@github.com> wrote:

Yup, it’s the master branch. Sounds good!

On Jan 7, 2016, at 4:56 PM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Hi James!

Just to be sure I get the right one, I am cloning the master branch on https://github.com/SeismicData/asdf-library...just correct me if I need another branch. I'll try again first thing tomorrow morning! Best Laura

Institut f�r Geophysik, ETH Z�rich Laura Ermert (PhD student) NO H 52.2 8092 Z�rich Schweiz

From: James Smith [notifications@github.commailto:notifications@github.commailto:notifications@github.com] Sent: Thursday, January 07, 2016 8:13 PM To: SeismicData/asdf-library Cc: Ermert Laura Subject: Re: [asdf-library] specfem3d_globe output to asdf very slow (#16)

Can you try again? Also, please double check you compiled and linked to the latest asdf-lib.

Thanks, James

On Jan 7, 2016, at 12:55 PM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

No problem! Thanks a lot :) (at least I know again how to compile, haha)

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

On 07 Jan 2016, at 18:51, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Laura,

It looks like my merge of the original_ASDF branch that has the working writer to the devel branch on github didn�t work. Sorry about that.

It looks like the old writer is still on the devel branch. I will fix it later today and update you.

Cheers, James

On Jan 7, 2016, at 11:22 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Hi James!

It took me a while to recompile everything � had to remember how to do that, which should be faster now in the future. Unfortunately when I ran it on a 20-minute seismogram test, I received a bunch of error messages: The synthetics.h5 file is opened, but then the waveforms not successfully written, although the station names are successfully included. Let me know if I can change something to make it work. Cheers! Laura

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2HDF5-DIAG: Error detected in HDF5 (1.8.14) : MPI-process 1 #000: H5D.c line 165 in H5Dcreate2(): not a location ID : major: Invalid arguments to routine minor: Inappropriate type

000: H5D.c line 165 in H5Dcreate2(): not a location ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Bad value

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0HDF5-DIAG: Error detected in HDF5 (1.8.14) : HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2MPI-process 1:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

major: Invalid arguments to routine

000: H5D.c line 165 in H5Dcreate2(): not a location ID

minor: Inappropriate type major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Inappropriate type

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

minor: Bad value major: Invalid arguments to routine major: Invalid arguments to routine minor: Bad value minor: Bad value

�.. Etc, etc, etc �.

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5F.c line 795 in H5Fclose(): decrementing file ID failed

major: Object atom minor: Unable to close file

001: H5I.c line 1475 in H5I_dec_app_ref(): can't decrement ID ref count

major: Object atom minor: Unable to decrement reference count

002: H5Fint.c line 1251 in H5F_close(): can't close file, there are objects still open

major: File accessibilty

minor: Unable to close file

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169714255.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169755077.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169756157.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169777531.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169818791.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169823136.

ghost commented 8 years ago

Hi Laura,

I’ve seen this error before when I used an older version of write_output_ASDF.f90, so I thought it was related to that. I’ll test a fresh clone of the repo here.

I’m using an older version of hdf5 here (1.8.10), but I don’t think that is a problem. The other test I can try is on a different cluster. I should have time today to try it.

James

On Jan 8, 2016, at 5:39 AM, lermert notifications@github.com<mailto:notifications@github.com> wrote:

Hi James,

unfortunately, still the same. I used the master branch at asdf-library, deleted my old executable, compiled, linked against this one during specfem compilation, compiled specfem, but no change.

Do you think it could be related to the settings I use for compilation? I pasted the module list below, the last few are the ones I loaded for compiling asdf. cheers from over here, Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

1) modules/3.2.10.3 2) eswrap/1.1.0-1.020200.1231.0 3) switch/1.0-1.0502.60522.1.61.ari 4) craype-network-aries 5) gcc/4.8.2 6) craype/2.4.0 7) craype-sandybridge 8) slurm 9) cray-mpich/7.2.2 10) alps/5.2.4-2.0502.9822.32.1.ari 11) ddt/5.1 12) cudatoolkit/6.5.14-1.0502.9836.8.1 13) totalview-support/1.1.4 14) totalview/8.11.0 15) cray-libsci/13.0.4 16) udreg/2.3.2-1.0502.10518.2.17.ari 17) ugni/6.0-1.0502.10863.8.29.ari 18) pmi/5.0.7-1.0000.10678.155.25.ari 19) dmapp/7.0.1-1.0502.11080.8.76.ari 20) gni-headers/4.0-1.0502.10859.7.8.ari 21) xpmem/0.1-2.0502.64982.5.3.ari 22) dvs/2.5_0.9.0-1.0502.2188.1.116.ari 23) alps/5.2.4-2.0502.9774.31.11.ari 24) rca/1.0.0-2.0502.60530.1.62.ari 25) atp/1.8.2 26) PrgEnv-gnu/5.2.82 27) cmake/3.3.2 28) cray-hdf5-parallel/1.8.14 29) boost/1.58.0

On 07 Jan 2016, at 23:13, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Yup, it’s the master branch. Sounds good!

On Jan 7, 2016, at 4:56 PM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi James!

Just to be sure I get the right one, I am cloning the master branch on https://github.com/SeismicData/asdf-library...just correct me if I need another branch. I'll try again first thing tomorrow morning! Best Laura

Institut f�r Geophysik, ETH Z�rich Laura Ermert (PhD student) NO H 52.2 8092 Z�rich Schweiz

From: James Smith [notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com] Sent: Thursday, January 07, 2016 8:13 PM To: SeismicData/asdf-library Cc: Ermert Laura Subject: Re: [asdf-library] specfem3d_globe output to asdf very slow (#16)

Can you try again? Also, please double check you compiled and linked to the latest asdf-lib.

Thanks, James

On Jan 7, 2016, at 12:55 PM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

No problem! Thanks a lot :) (at least I know again how to compile, haha)

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

On 07 Jan 2016, at 18:51, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Laura,

It looks like my merge of the original_ASDF branch that has the working writer to the devel branch on github didn�t work. Sorry about that.

It looks like the old writer is still on the devel branch. I will fix it later today and update you.

Cheers, James

On Jan 7, 2016, at 11:22 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Hi James!

It took me a while to recompile everything � had to remember how to do that, which should be faster now in the future. Unfortunately when I ran it on a 20-minute seismogram test, I received a bunch of error messages: The synthetics.h5 file is opened, but then the waveforms not successfully written, although the station names are successfully included. Let me know if I can change something to make it work. Cheers! Laura

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2HDF5-DIAG: Error detected in HDF5 (1.8.14) : MPI-process 1 #000: H5D.c line 165 in H5Dcreate2(): not a location ID : major: Invalid arguments to routine minor: Inappropriate type

000: H5D.c line 165 in H5Dcreate2(): not a location ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Bad value

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0HDF5-DIAG: Error detected in HDF5 (1.8.14) : HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2MPI-process 1:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

major: Invalid arguments to routine

000: H5D.c line 165 in H5Dcreate2(): not a location ID

minor: Inappropriate type major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Inappropriate type

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

minor: Bad value major: Invalid arguments to routine major: Invalid arguments to routine minor: Bad value minor: Bad value

�.. Etc, etc, etc �.

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5F.c line 795 in H5Fclose(): decrementing file ID failed

major: Object atom minor: Unable to close file

001: H5I.c line 1475 in H5I_dec_app_ref(): can't decrement ID ref count

major: Object atom minor: Unable to decrement reference count

002: H5Fint.c line 1251 in H5F_close(): can't close file, there are objects still open

major: File accessibilty

minor: Unable to close file

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169714255.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169755077.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169756157.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169777531.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169818791.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169823136.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169959380.

lermert commented 8 years ago

Hi James!

I think I might have an idea of the problem. Actually, as I watched the configuration of asdf I saw it does not use the cray-hdf5-parallel, but another hdf5 located in my anaconda directory. Is there a way to tell cmake not to use that hdf5, but rather the cray-hdf5-parallel? For now I will just remove and reinstall anaconda. Best Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 08 Jan 2016, at 16:53, James Smith notifications@github.com<mailto:notifications@github.com> wrote:

Hi Laura,

I’ve seen this error before when I used an older version of write_output_ASDF.f90, so I thought it was related to that. I’ll test a fresh clone of the repo here.

I’m using an older version of hdf5 here (1.8.10), but I don’t think that is a problem. The other test I can try is on a different cluster. I should have time today to try it.

James

On Jan 8, 2016, at 5:39 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Hi James,

unfortunately, still the same. I used the master branch at asdf-library, deleted my old executable, compiled, linked against this one during specfem compilation, compiled specfem, but no change.

Do you think it could be related to the settings I use for compilation? I pasted the module list below, the last few are the ones I loaded for compiling asdf. cheers from over here, Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

1) modules/3.2.10.3 2) eswrap/1.1.0-1.020200.1231.0 3) switch/1.0-1.0502.60522.1.61.ari 4) craype-network-aries 5) gcc/4.8.2 6) craype/2.4.0 7) craype-sandybridge 8) slurm 9) cray-mpich/7.2.2 10) alps/5.2.4-2.0502.9822.32.1.ari 11) ddt/5.1 12) cudatoolkit/6.5.14-1.0502.9836.8.1 13) totalview-support/1.1.4 14) totalview/8.11.0 15) cray-libsci/13.0.4 16) udreg/2.3.2-1.0502.10518.2.17.ari 17) ugni/6.0-1.0502.10863.8.29.ari 18) pmi/5.0.7-1.0000.10678.155.25.ari 19) dmapp/7.0.1-1.0502.11080.8.76.ari 20) gni-headers/4.0-1.0502.10859.7.8.ari 21) xpmem/0.1-2.0502.64982.5.3.ari 22) dvs/2.5_0.9.0-1.0502.2188.1.116.ari 23) alps/5.2.4-2.0502.9774.31.11.ari 24) rca/1.0.0-2.0502.60530.1.62.ari 25) atp/1.8.2 26) PrgEnv-gnu/5.2.82 27) cmake/3.3.2 28) cray-hdf5-parallel/1.8.14 29) boost/1.58.0

On 07 Jan 2016, at 23:13, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Yup, it’s the master branch. Sounds good!

On Jan 7, 2016, at 4:56 PM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi James!

Just to be sure I get the right one, I am cloning the master branch on https://github.com/SeismicData/asdf-library...just correct me if I need another branch. I'll try again first thing tomorrow morning! Best Laura

Institut f�r Geophysik, ETH Z�rich Laura Ermert (PhD student) NO H 52.2 8092 Z�rich Schweiz

From: James Smith [notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com] Sent: Thursday, January 07, 2016 8:13 PM To: SeismicData/asdf-library Cc: Ermert Laura Subject: Re: [asdf-library] specfem3d_globe output to asdf very slow (#16)

Can you try again? Also, please double check you compiled and linked to the latest asdf-lib.

Thanks, James

On Jan 7, 2016, at 12:55 PM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

No problem! Thanks a lot :) (at least I know again how to compile, haha)

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

On 07 Jan 2016, at 18:51, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Laura,

It looks like my merge of the original_ASDF branch that has the working writer to the devel branch on github didn�t work. Sorry about that.

It looks like the old writer is still on the devel branch. I will fix it later today and update you.

Cheers, James

On Jan 7, 2016, at 11:22 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Hi James!

It took me a while to recompile everything � had to remember how to do that, which should be faster now in the future. Unfortunately when I ran it on a 20-minute seismogram test, I received a bunch of error messages: The synthetics.h5 file is opened, but then the waveforms not successfully written, although the station names are successfully included. Let me know if I can change something to make it work. Cheers! Laura

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2HDF5-DIAG: Error detected in HDF5 (1.8.14) : MPI-process 1 #000: H5D.c line 165 in H5Dcreate2(): not a location ID : major: Invalid arguments to routine minor: Inappropriate type

000: H5D.c line 165 in H5Dcreate2(): not a location ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Bad value

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0HDF5-DIAG: Error detected in HDF5 (1.8.14) : HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2MPI-process 1:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

major: Invalid arguments to routine

000: H5D.c line 165 in H5Dcreate2(): not a location ID

minor: Inappropriate type major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Inappropriate type

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

minor: Bad value major: Invalid arguments to routine major: Invalid arguments to routine minor: Bad value minor: Bad value

�.. Etc, etc, etc �.

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5F.c line 795 in H5Fclose(): decrementing file ID failed

major: Object atom minor: Unable to close file

001: H5I.c line 1475 in H5I_dec_app_ref(): can't decrement ID ref count

major: Object atom minor: Unable to decrement reference count

002: H5Fint.c line 1251 in H5F_close(): can't close file, there are objects still open

major: File accessibilty

minor: Unable to close file

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169714255.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169755077.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169756157.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169777531.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169818791.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169823136.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169959380.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-170037690.

lermert commented 8 years ago

Hi again,

sorry, my last question was probably stupid. I guess I can just prepend the path of the hdf5 I would like.

I compiled now with an older hdf5 library, but still get the same. Let me know what you find out…cheers Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 08 Jan 2016, at 16:53, James Smith notifications@github.com<mailto:notifications@github.com> wrote:

Hi Laura,

I’ve seen this error before when I used an older version of write_output_ASDF.f90, so I thought it was related to that. I’ll test a fresh clone of the repo here.

I’m using an older version of hdf5 here (1.8.10), but I don’t think that is a problem. The other test I can try is on a different cluster. I should have time today to try it.

James

On Jan 8, 2016, at 5:39 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Hi James,

unfortunately, still the same. I used the master branch at asdf-library, deleted my old executable, compiled, linked against this one during specfem compilation, compiled specfem, but no change.

Do you think it could be related to the settings I use for compilation? I pasted the module list below, the last few are the ones I loaded for compiling asdf. cheers from over here, Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

1) modules/3.2.10.3 2) eswrap/1.1.0-1.020200.1231.0 3) switch/1.0-1.0502.60522.1.61.ari 4) craype-network-aries 5) gcc/4.8.2 6) craype/2.4.0 7) craype-sandybridge 8) slurm 9) cray-mpich/7.2.2 10) alps/5.2.4-2.0502.9822.32.1.ari 11) ddt/5.1 12) cudatoolkit/6.5.14-1.0502.9836.8.1 13) totalview-support/1.1.4 14) totalview/8.11.0 15) cray-libsci/13.0.4 16) udreg/2.3.2-1.0502.10518.2.17.ari 17) ugni/6.0-1.0502.10863.8.29.ari 18) pmi/5.0.7-1.0000.10678.155.25.ari 19) dmapp/7.0.1-1.0502.11080.8.76.ari 20) gni-headers/4.0-1.0502.10859.7.8.ari 21) xpmem/0.1-2.0502.64982.5.3.ari 22) dvs/2.5_0.9.0-1.0502.2188.1.116.ari 23) alps/5.2.4-2.0502.9774.31.11.ari 24) rca/1.0.0-2.0502.60530.1.62.ari 25) atp/1.8.2 26) PrgEnv-gnu/5.2.82 27) cmake/3.3.2 28) cray-hdf5-parallel/1.8.14 29) boost/1.58.0

On 07 Jan 2016, at 23:13, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Yup, it’s the master branch. Sounds good!

On Jan 7, 2016, at 4:56 PM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi James!

Just to be sure I get the right one, I am cloning the master branch on https://github.com/SeismicData/asdf-library...just correct me if I need another branch. I'll try again first thing tomorrow morning! Best Laura

Institut f�r Geophysik, ETH Z�rich Laura Ermert (PhD student) NO H 52.2 8092 Z�rich Schweiz

From: James Smith [notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com] Sent: Thursday, January 07, 2016 8:13 PM To: SeismicData/asdf-library Cc: Ermert Laura Subject: Re: [asdf-library] specfem3d_globe output to asdf very slow (#16)

Can you try again? Also, please double check you compiled and linked to the latest asdf-lib.

Thanks, James

On Jan 7, 2016, at 12:55 PM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

No problem! Thanks a lot :) (at least I know again how to compile, haha)

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

On 07 Jan 2016, at 18:51, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Laura,

It looks like my merge of the original_ASDF branch that has the working writer to the devel branch on github didn�t work. Sorry about that.

It looks like the old writer is still on the devel branch. I will fix it later today and update you.

Cheers, James

On Jan 7, 2016, at 11:22 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Hi James!

It took me a while to recompile everything � had to remember how to do that, which should be faster now in the future. Unfortunately when I ran it on a 20-minute seismogram test, I received a bunch of error messages: The synthetics.h5 file is opened, but then the waveforms not successfully written, although the station names are successfully included. Let me know if I can change something to make it work. Cheers! Laura

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2HDF5-DIAG: Error detected in HDF5 (1.8.14) : MPI-process 1 #000: H5D.c line 165 in H5Dcreate2(): not a location ID : major: Invalid arguments to routine minor: Inappropriate type

000: H5D.c line 165 in H5Dcreate2(): not a location ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Bad value

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0HDF5-DIAG: Error detected in HDF5 (1.8.14) : HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2MPI-process 1:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

major: Invalid arguments to routine

000: H5D.c line 165 in H5Dcreate2(): not a location ID

minor: Inappropriate type major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Inappropriate type

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

minor: Bad value major: Invalid arguments to routine major: Invalid arguments to routine minor: Bad value minor: Bad value

�.. Etc, etc, etc �.

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5F.c line 795 in H5Fclose(): decrementing file ID failed

major: Object atom minor: Unable to close file

001: H5I.c line 1475 in H5I_dec_app_ref(): can't decrement ID ref count

major: Object atom minor: Unable to decrement reference count

002: H5Fint.c line 1251 in H5F_close(): can't close file, there are objects still open

major: File accessibilty

minor: Unable to close file

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169714255.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169755077.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169756157.

� Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169777531.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169818791.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169823136.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-169959380.

— Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/16#issuecomment-170037690.

ghost commented 8 years ago

Hi Laura,

The fresh clone works for me. I am having some issues with gnu compilers, but that doesn’t explain your error. Are you using the default Par_fie and STATIONS file?

Thanks, James

On Jan 8, 2016, at 12:13 PM, lermert notifications@github.com<mailto:notifications@github.com> wrote:

Hi again,

sorry, my last question was probably stupid. I guess I can just prepend the path of the hdf5 I would like.

I compiled now with an older hdf5 library, but still get the same. Let me know what you find out…cheers Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

On 08 Jan 2016, at 16:53, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Laura,

I’ve seen this error before when I used an older version of write_output_ASDF.f90, so I thought it was related to that. I’ll test a fresh clone of the repo here.

I’m using an older version of hdf5 here (1.8.10), but I don’t think that is a problem. The other test I can try is on a different cluster. I should have time today to try it.

James

On Jan 8, 2016, at 5:39 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi James,

unfortunately, still the same. I used the master branch at asdf-library, deleted my old executable, compiled, linked against this one during specfem compilation, compiled specfem, but no change.

Do you think it could be related to the settings I use for compilation? I pasted the module list below, the last few are the ones I loaded for compiling asdf. cheers from over here, Laura

Laura Ermert PhD student Institut für Geophysik ETH Zürich

Sonneggstrasse 5, NO H 39.3 CH 8092 Zürich

1) modules/3.2.10.3 2) eswrap/1.1.0-1.020200.1231.0 3) switch/1.0-1.0502.60522.1.61.ari 4) craype-network-aries 5) gcc/4.8.2 6) craype/2.4.0 7) craype-sandybridge 8) slurm 9) cray-mpich/7.2.2 10) alps/5.2.4-2.0502.9822.32.1.ari 11) ddt/5.1 12) cudatoolkit/6.5.14-1.0502.9836.8.1 13) totalview-support/1.1.4 14) totalview/8.11.0 15) cray-libsci/13.0.4 16) udreg/2.3.2-1.0502.10518.2.17.ari 17) ugni/6.0-1.0502.10863.8.29.ari 18) pmi/5.0.7-1.0000.10678.155.25.ari 19) dmapp/7.0.1-1.0502.11080.8.76.ari 20) gni-headers/4.0-1.0502.10859.7.8.ari 21) xpmem/0.1-2.0502.64982.5.3.ari 22) dvs/2.5_0.9.0-1.0502.2188.1.116.ari 23) alps/5.2.4-2.0502.9774.31.11.ari 24) rca/1.0.0-2.0502.60530.1.62.ari 25) atp/1.8.2 26) PrgEnv-gnu/5.2.82 27) cmake/3.3.2 28) cray-hdf5-parallel/1.8.14 29) boost/1.58.0

On 07 Jan 2016, at 23:13, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Yup, it’s the master branch. Sounds good!

On Jan 7, 2016, at 4:56 PM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi James!

Just to be sure I get the right one, I am cloning the master branch on https://github.com/SeismicData/asdf-library...just correct me if I need another branch. I'll try again first thing tomorrow morning! Best Laura

Institut f�r Geophysik, ETH Z�rich Laura Ermert (PhD student) NO H 52.2 8092 Z�rich Schweiz

From: James Smith [notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com] Sent: Thursday, January 07, 2016 8:13 PM To: SeismicData/asdf-library Cc: Ermert Laura Subject: Re: [asdf-library] specfem3d_globe output to asdf very slow (#16)

Can you try again? Also, please double check you compiled and linked to the latest asdf-lib.

Thanks, James

On Jan 7, 2016, at 12:55 PM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

No problem! Thanks a lot :) (at least I know again how to compile, haha)

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

On 07 Jan 2016, at 18:51, James Smith notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Laura,

It looks like my merge of the original_ASDF branch that has the working writer to the devel branch on github didn�t work. Sorry about that.

It looks like the old writer is still on the devel branch. I will fix it later today and update you.

Cheers, James

On Jan 7, 2016, at 11:22 AM, lermert notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi Hi James!

It took me a while to recompile everything � had to remember how to do that, which should be faster now in the future. Unfortunately when I ran it on a 20-minute seismogram test, I received a bunch of error messages: The synthetics.h5 file is opened, but then the waveforms not successfully written, although the station names are successfully included. Let me know if I can change something to make it work. Cheers! Laura

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2HDF5-DIAG: Error detected in HDF5 (1.8.14) : MPI-process 1 #000: H5D.c line 165 in H5Dcreate2(): not a location ID : major: Invalid arguments to routine minor: Inappropriate type

000: H5D.c line 165 in H5Dcreate2(): not a location ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Bad value

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0HDF5-DIAG: Error detected in HDF5 (1.8.14) : HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 2MPI-process 1:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

:

000: H5D.c line 165 in H5Dcreate2(): not a location ID

major: Invalid arguments to routine

000: H5D.c line 165 in H5Dcreate2(): not a location ID

minor: Inappropriate type major: Invalid arguments to routine major: Invalid arguments to routine minor: Inappropriate type minor: Inappropriate type

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

major: Invalid arguments to routine

001: H5Gloc.c line 253 in H5G_loc(): invalid object ID

minor: Bad value major: Invalid arguments to routine major: Invalid arguments to routine minor: Bad value minor: Bad value

�.. Etc, etc, etc �.

HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5D.c line 415 in H5Dclose(): not a dataset

major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 16:

000: H5F.c line 795 in H5Fclose(): decrementing file ID failed

major: Object atom minor: Unable to close file

001: H5I.c line 1475 in H5I_dec_app_ref(): can't decrement ID ref count

major: Object atom minor: Unable to decrement reference count

002: H5Fint.c line 1251 in H5F_close(): can't close file, there are objects still open

major: File accessibilty

minor: Unable to close file

Laura Ermert PhD student Institut f�r Geophysik ETH Z�rich

Sonneggstrasse 5, NO H 39.3 CH 8092 Z�rich

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