SLEPc: HDF5 support for SVD/EPSValuesView?
Hello In SLEPc one may write singular vectors to an HDF5 file using SVDVectorsView(), but a similar option doesn't seem to work for singular values using SVDValuesView(). The values are viewed correctly using other viewers, but nothing is seemingly produced when using an HDF5 viewer. Looking at the source code seems to confirm this, and suggests that there is a similar situation with EPS. Is this correct, and if so, might there be plans to include such functionality in future releases? Med venlig hilsen / Best Regards Peder Jørgensgaard Olesen PhD Student, Turbulence Research Lab Dept. of Mechanical Engineering Technical University of Denmark Koppels Allé Bygning 403, Rum 105 DK-2800 Kgs. Lyngby
I could try and adapt the HDF5 code in PETSc for this, but I am no HDF5 expert. Furthermore I am busy at the moment, so it is faster if you could prepare a merge request with this addition. Jose
El 4 jun 2021, a las 13:10, Peder Jørgensgaard Olesen via petsc-users <[email protected]> escribió:
Hello
In SLEPc one may write singular vectors to an HDF5 file using SVDVectorsView(), but a similar option doesn't seem to work for singular values using SVDValuesView(). The values are viewed correctly using other viewers, but nothing is seemingly produced when using an HDF5 viewer. Looking at the source code seems to confirm this, and suggests that there is a similar situation with EPS.
Is this correct, and if so, might there be plans to include such functionality in future releases?
Med venlig hilsen / Best Regards
Peder Jørgensgaard Olesen PhD Student, Turbulence Research Lab Dept. of Mechanical Engineering Technical University of Denmark Koppels Allé Bygning 403, Rum 105 DK-2800 Kgs. Lyngby
On Fri, Jun 4, 2021 at 9:31 AM Jose E. Roman <[email protected]> wrote:
I could try and adapt the HDF5 code in PETSc for this, but I am no HDF5 expert. Furthermore I am busy at the moment, so it is faster if you could prepare a merge request with this addition.
I think the easiest thing is to wrap a Vec around the values and just VecView() it into the same HDF5 file. THanks, Matt
Jose
El 4 jun 2021, a las 13:10, Peder Jørgensgaard Olesen via petsc-users < [email protected]> escribió:
Hello
In SLEPc one may write singular vectors to an HDF5 file using SVDVectorsView(), but a similar option doesn't seem to work for singular values using SVDValuesView(). The values are viewed correctly using other viewers, but nothing is seemingly produced when using an HDF5 viewer. Looking at the source code seems to confirm this, and suggests that there is a similar situation with EPS.
Is this correct, and if so, might there be plans to include such functionality in future releases?
Med venlig hilsen / Best Regards
Peder Jørgensgaard Olesen PhD Student, Turbulence Research Lab Dept. of Mechanical Engineering Technical University of Denmark Koppels Allé Bygning 403, Rum 105 DK-2800 Kgs. Lyngby
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
The problem is that here I am writing PetscReal's not PetscScalar's, and in EPS I am writing PetscComplex even in real scalars. That is why I did not implement it as you are suggesting. Jose
El 4 jun 2021, a las 15:56, Matthew Knepley <[email protected]> escribió:
On Fri, Jun 4, 2021 at 9:31 AM Jose E. Roman <[email protected]> wrote: I could try and adapt the HDF5 code in PETSc for this, but I am no HDF5 expert. Furthermore I am busy at the moment, so it is faster if you could prepare a merge request with this addition.
I think the easiest thing is to wrap a Vec around the values and just VecView() it into the same HDF5 file.
THanks,
Matt
Jose
El 4 jun 2021, a las 13:10, Peder Jørgensgaard Olesen via petsc-users <[email protected]> escribió:
Hello
In SLEPc one may write singular vectors to an HDF5 file using SVDVectorsView(), but a similar option doesn't seem to work for singular values using SVDValuesView(). The values are viewed correctly using other viewers, but nothing is seemingly produced when using an HDF5 viewer. Looking at the source code seems to confirm this, and suggests that there is a similar situation with EPS.
Is this correct, and if so, might there be plans to include such functionality in future releases?
Med venlig hilsen / Best Regards
Peder Jørgensgaard Olesen PhD Student, Turbulence Research Lab Dept. of Mechanical Engineering Technical University of Denmark Koppels Allé Bygning 403, Rum 105 DK-2800 Kgs. Lyngby
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
What Matt suggests could perhaps be used as a workaround, though it appears neither elegant nor in my experience efficient. I may be wrong on this. My attempted solution was to use a binary viewer instead, but I can't find a clear way to retrieve values thus stored with PETSc, as these do not lend themselves to be read using VecLoad. Again one might go about that by wrapping them inside a vector and send that to the viewer, which just brings us back around to the original problem. - Peder ________________________________ Fra: Jose E. Roman <[email protected]> Sendt: 4. juni 2021 16:01:04 Til: Matthew Knepley Cc: Peder Jørgensgaard Olesen; [email protected] Emne: Re: [petsc-users] SLEPc: HDF5 support for SVD/EPSValuesView? The problem is that here I am writing PetscReal's not PetscScalar's, and in EPS I am writing PetscComplex even in real scalars. That is why I did not implement it as you are suggesting. Jose
El 4 jun 2021, a las 15:56, Matthew Knepley <[email protected]> escribió:
On Fri, Jun 4, 2021 at 9:31 AM Jose E. Roman <[email protected]> wrote: I could try and adapt the HDF5 code in PETSc for this, but I am no HDF5 expert. Furthermore I am busy at the moment, so it is faster if you could prepare a merge request with this addition.
I think the easiest thing is to wrap a Vec around the values and just VecView() it into the same HDF5 file.
THanks,
Matt
Jose
El 4 jun 2021, a las 13:10, Peder Jørgensgaard Olesen via petsc-users <[email protected]> escribió:
Hello
In SLEPc one may write singular vectors to an HDF5 file using SVDVectorsView(), but a similar option doesn't seem to work for singular values using SVDValuesView(). The values are viewed correctly using other viewers, but nothing is seemingly produced when using an HDF5 viewer. Looking at the source code seems to confirm this, and suggests that there is a similar situation with EPS.
Is this correct, and if so, might there be plans to include such functionality in future releases?
Med venlig hilsen / Best Regards
Peder Jørgensgaard Olesen PhD Student, Turbulence Research Lab Dept. of Mechanical Engineering Technical University of Denmark Koppels Allé Bygning 403, Rum 105 DK-2800 Kgs. Lyngby
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
On Fri, Jun 4, 2021 at 10:28 AM Peder Jørgensgaard Olesen <[email protected]> wrote:
What Matt suggests could perhaps be used as a workaround, though it appears neither elegant nor in my experience efficient. I may be wrong on this.
Why is it not efficient? Thanks, Matt
My attempted solution was to use a binary viewer instead, but I can't find a clear way to retrieve values thus stored with PETSc, as these do not lend themselves to be read using VecLoad. Again one might go about that by wrapping them inside a vector and send that to the viewer, which just brings us back around to the original problem.
- Peder ------------------------------ *Fra:* Jose E. Roman <[email protected]> *Sendt:* 4. juni 2021 16:01:04 *Til:* Matthew Knepley *Cc:* Peder Jørgensgaard Olesen; [email protected] *Emne:* Re: [petsc-users] SLEPc: HDF5 support for SVD/EPSValuesView?
The problem is that here I am writing PetscReal's not PetscScalar's, and in EPS I am writing PetscComplex even in real scalars. That is why I did not implement it as you are suggesting.
Jose
El 4 jun 2021, a las 15:56, Matthew Knepley <[email protected]> escribió:
On Fri, Jun 4, 2021 at 9:31 AM Jose E. Roman <[email protected]> wrote: I could try and adapt the HDF5 code in PETSc for this, but I am no HDF5 expert. Furthermore I am busy at the moment, so it is faster if you could prepare a merge request with this addition.
I think the easiest thing is to wrap a Vec around the values and just VecView() it into the same HDF5 file.
THanks,
Matt
Jose
El 4 jun 2021, a las 13:10, Peder Jørgensgaard Olesen via petsc-users < [email protected]> escribió:
Hello
In SLEPc one may write singular vectors to an HDF5 file using SVDVectorsView(), but a similar option doesn't seem to work for singular values using SVDValuesView(). The values are viewed correctly using other viewers, but nothing is seemingly produced when using an HDF5 viewer. Looking at the source code seems to confirm this, and suggests that there is a similar situation with EPS.
Is this correct, and if so, might there be plans to include such functionality in future releases?
Med venlig hilsen / Best Regards
Peder Jørgensgaard Olesen PhD Student, Turbulence Research Lab Dept. of Mechanical Engineering Technical University of Denmark Koppels Allé Bygning 403, Rum 105 DK-2800 Kgs. Lyngby
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
Excellent question. It may well be some quirk of my own setup that somehow makes VecView run rather sluggishly, making it hardly relevant to the general case. - Peder ________________________________ Fra: Matthew Knepley <[email protected]> Sendt: 4. juni 2021 16:48:05 Til: Peder Jørgensgaard Olesen Cc: Jose E. Roman; [email protected] Emne: Re: [petsc-users] SLEPc: HDF5 support for SVD/EPSValuesView? On Fri, Jun 4, 2021 at 10:28 AM Peder Jørgensgaard Olesen <[email protected]<mailto:[email protected]>> wrote: What Matt suggests could perhaps be used as a workaround, though it appears neither elegant nor in my experience efficient. I may be wrong on this. Why is it not efficient? Thanks, Matt My attempted solution was to use a binary viewer instead, but I can't find a clear way to retrieve values thus stored with PETSc, as these do not lend themselves to be read using VecLoad. Again one might go about that by wrapping them inside a vector and send that to the viewer, which just brings us back around to the original problem. - Peder ________________________________ Fra: Jose E. Roman <[email protected]<mailto:[email protected]>> Sendt: 4. juni 2021 16:01:04 Til: Matthew Knepley Cc: Peder Jørgensgaard Olesen; [email protected]<mailto:[email protected]> Emne: Re: [petsc-users] SLEPc: HDF5 support for SVD/EPSValuesView? The problem is that here I am writing PetscReal's not PetscScalar's, and in EPS I am writing PetscComplex even in real scalars. That is why I did not implement it as you are suggesting. Jose
El 4 jun 2021, a las 15:56, Matthew Knepley <[email protected]<mailto:[email protected]>> escribió:
On Fri, Jun 4, 2021 at 9:31 AM Jose E. Roman <[email protected]<mailto:[email protected]>> wrote: I could try and adapt the HDF5 code in PETSc for this, but I am no HDF5 expert. Furthermore I am busy at the moment, so it is faster if you could prepare a merge request with this addition.
I think the easiest thing is to wrap a Vec around the values and just VecView() it into the same HDF5 file.
THanks,
Matt
Jose
El 4 jun 2021, a las 13:10, Peder Jørgensgaard Olesen via petsc-users <[email protected]<mailto:[email protected]>> escribió:
Hello
In SLEPc one may write singular vectors to an HDF5 file using SVDVectorsView(), but a similar option doesn't seem to work for singular values using SVDValuesView(). The values are viewed correctly using other viewers, but nothing is seemingly produced when using an HDF5 viewer. Looking at the source code seems to confirm this, and suggests that there is a similar situation with EPS.
Is this correct, and if so, might there be plans to include such functionality in future releases?
Med venlig hilsen / Best Regards
Peder Jørgensgaard Olesen PhD Student, Turbulence Research Lab Dept. of Mechanical Engineering Technical University of Denmark Koppels Allé Bygning 403, Rum 105 DK-2800 Kgs. Lyngby
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<http://www.cse.buffalo.edu/~knepley/>
On Fri, Jun 4, 2021 at 10:59 AM Peder Jørgensgaard Olesen <[email protected]> wrote:
Excellent question. It may well be some quirk of my own setup that somehow makes VecView run rather sluggishly, making it hardly relevant to the general case.
Maybe I can help speed things up for you. Is this in serial or parallel? Is the vector big or small? Is it possible to send the output of -log_view? Thanks Matt
- Peder ------------------------------ *Fra:* Matthew Knepley <[email protected]> *Sendt:* 4. juni 2021 16:48:05 *Til:* Peder Jørgensgaard Olesen *Cc:* Jose E. Roman; [email protected] *Emne:* Re: [petsc-users] SLEPc: HDF5 support for SVD/EPSValuesView?
On Fri, Jun 4, 2021 at 10:28 AM Peder Jørgensgaard Olesen < [email protected]> wrote:
What Matt suggests could perhaps be used as a workaround, though it appears neither elegant nor in my experience efficient. I may be wrong on this.
Why is it not efficient?
Thanks,
Matt
My attempted solution was to use a binary viewer instead, but I can't find a clear way to retrieve values thus stored with PETSc, as these do not lend themselves to be read using VecLoad. Again one might go about that by wrapping them inside a vector and send that to the viewer, which just brings us back around to the original problem.
- Peder ------------------------------ *Fra:* Jose E. Roman <[email protected]> *Sendt:* 4. juni 2021 16:01:04 *Til:* Matthew Knepley *Cc:* Peder Jørgensgaard Olesen; [email protected] *Emne:* Re: [petsc-users] SLEPc: HDF5 support for SVD/EPSValuesView?
The problem is that here I am writing PetscReal's not PetscScalar's, and in EPS I am writing PetscComplex even in real scalars. That is why I did not implement it as you are suggesting.
Jose
El 4 jun 2021, a las 15:56, Matthew Knepley <[email protected]> escribió:
On Fri, Jun 4, 2021 at 9:31 AM Jose E. Roman <[email protected]> wrote: I could try and adapt the HDF5 code in PETSc for this, but I am no HDF5 expert. Furthermore I am busy at the moment, so it is faster if you could prepare a merge request with this addition.
I think the easiest thing is to wrap a Vec around the values and just VecView() it into the same HDF5 file.
THanks,
Matt
Jose
El 4 jun 2021, a las 13:10, Peder Jørgensgaard Olesen via petsc-users <[email protected]> escribió:
Hello
In SLEPc one may write singular vectors to an HDF5 file using SVDVectorsView(), but a similar option doesn't seem to work for singular values using SVDValuesView(). The values are viewed correctly using other viewers, but nothing is seemingly produced when using an HDF5 viewer. Looking at the source code seems to confirm this, and suggests that there is a similar situation with EPS.
Is this correct, and if so, might there be plans to include such functionality in future releases?
Med venlig hilsen / Best Regards
Peder Jørgensgaard Olesen PhD Student, Turbulence Research Lab Dept. of Mechanical Engineering Technical University of Denmark Koppels Allé Bygning 403, Rum 105 DK-2800 Kgs. Lyngby
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
I have implemented a solution in https://gitlab.com/slepc/slepc/-/merge_requests/234 Let me know if you have suggestions. Jose
El 4 jun 2021, a las 17:38, Matthew Knepley <[email protected]> escribió:
On Fri, Jun 4, 2021 at 10:59 AM Peder Jørgensgaard Olesen <[email protected]> wrote: Excellent question. It may well be some quirk of my own setup that somehow makes VecView run rather sluggishly, making it hardly relevant to the general case.
Maybe I can help speed things up for you. Is this in serial or parallel? Is the vector big or small? Is it possible to send the output of -log_view?
Thanks
Matt - Peder
Fra: Matthew Knepley <[email protected]> Sendt: 4. juni 2021 16:48:05 Til: Peder Jørgensgaard Olesen Cc: Jose E. Roman; [email protected] Emne: Re: [petsc-users] SLEPc: HDF5 support for SVD/EPSValuesView?
On Fri, Jun 4, 2021 at 10:28 AM Peder Jørgensgaard Olesen <[email protected]> wrote: What Matt suggests could perhaps be used as a workaround, though it appears neither elegant nor in my experience efficient. I may be wrong on this.
Why is it not efficient?
Thanks,
Matt My attempted solution was to use a binary viewer instead, but I can't find a clear way to retrieve values thus stored with PETSc, as these do not lend themselves to be read using VecLoad. Again one might go about that by wrapping them inside a vector and send that to the viewer, which just brings us back around to the original problem.
- Peder
Fra: Jose E. Roman <[email protected]> Sendt: 4. juni 2021 16:01:04 Til: Matthew Knepley Cc: Peder Jørgensgaard Olesen; [email protected] Emne: Re: [petsc-users] SLEPc: HDF5 support for SVD/EPSValuesView?
The problem is that here I am writing PetscReal's not PetscScalar's, and in EPS I am writing PetscComplex even in real scalars. That is why I did not implement it as you are suggesting.
Jose
El 4 jun 2021, a las 15:56, Matthew Knepley <[email protected]> escribió:
On Fri, Jun 4, 2021 at 9:31 AM Jose E. Roman <[email protected]> wrote: I could try and adapt the HDF5 code in PETSc for this, but I am no HDF5 expert. Furthermore I am busy at the moment, so it is faster if you could prepare a merge request with this addition.
I think the easiest thing is to wrap a Vec around the values and just VecView() it into the same HDF5 file.
THanks,
Matt
Jose
El 4 jun 2021, a las 13:10, Peder Jørgensgaard Olesen via petsc-users <[email protected]> escribió:
Hello
In SLEPc one may write singular vectors to an HDF5 file using SVDVectorsView(), but a similar option doesn't seem to work for singular values using SVDValuesView(). The values are viewed correctly using other viewers, but nothing is seemingly produced when using an HDF5 viewer. Looking at the source code seems to confirm this, and suggests that there is a similar situation with EPS.
Is this correct, and if so, might there be plans to include such functionality in future releases?
Med venlig hilsen / Best Regards
Peder Jørgensgaard Olesen PhD Student, Turbulence Research Lab Dept. of Mechanical Engineering Technical University of Denmark Koppels Allé Bygning 403, Rum 105 DK-2800 Kgs. Lyngby
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
participants (3)
-
Jose E. Roman -
Matthew Knepley -
Peder Jørgensgaard Olesen