[Trilinos-Users] HDF5 - segmentation fault
Villa Andrea (RSE)
Andrea.Villa at rse-web.it
Thu Dec 27 02:17:25 MST 2012
I've got a segmentation fault also using the following driver: the use of hdf5 is very limited here.
Now I'm using the openMpi version 1.3 (standard ubuntu). I will install the 1.6 version and make some other tests.
Thank you.
#include <cmath>
#include <iostream>
#include "mpi.h"
#include "Epetra_MpiComm.h"
#include "Epetra_Map.h"
#include "EpetraExt_DistArray.h"
#include "EpetraExt_HDF5.h"
#include "Epetra_Import.h"
int main(int argc, char *argv[])
{
MPI_Init(&argc,&argv);
Epetra_MpiComm epetraComm(MPI_COMM_WORLD);
int numMyElements;
int MyGlobalElements[4];
if(epetraComm.MyPID() == 0)
{
numMyElements = 4;
MyGlobalElements[0] = 0;
MyGlobalElements[1] = 1;
MyGlobalElements[2] = 2;
MyGlobalElements[3] = 3;
}
if(epetraComm.MyPID() == 1)
{
numMyElements = 4;
MyGlobalElements[0] = 4;
MyGlobalElements[1] = 5;
MyGlobalElements[2] = 6;
MyGlobalElements[3] = 7;
}
if(epetraComm.MyPID() == 2)
{
numMyElements = 4;
MyGlobalElements[0] = 8;
MyGlobalElements[1] = 9;
MyGlobalElements[2] = 10;
MyGlobalElements[3] = 11;
}
if(epetraComm.MyPID() == 3)
{
numMyElements = 2;
MyGlobalElements[0] = 12;
MyGlobalElements[1] = 13;
}
string GroupName = "nodes";
Epetra_Map mappa(-1,numMyElements,MyGlobalElements,0,epetraComm);
EpetraExt::DistArray<double> nodes_epetra(mappa,3);
EpetraExt::HDF5 hdf5(epetraComm);
hdf5.Create("err.h5");
Epetra_Map LinearMap(mappa.NumGlobalElements(), mappa.IndexBase(), epetraComm);
Epetra_Import Importer(LinearMap, mappa);
EpetraExt::DistArray<double> LinearX(LinearMap, nodes_epetra.RowSize());
LinearX.Import(nodes_epetra, Importer, Insert);
hdf5.Close();
MPI_Finalize();
}
-----Original Message-----
From: Antonio Cervone [mailto:ant.cervone at gmail.com]
Sent: Wed 12/26/2012 11:27 AM
To: Villa Andrea (RSE)
Cc: trilinos-users at software.sandia.gov
Subject: Re: [Trilinos-Users] HDF5 - segmentation fault
after some more tests, i can say that it fails when the map has a
different number of local elements (if you change the assignment of
element for the 4th proc to 4 it will work) or if the row size is
greater than one.
it seems to be a bug in the hdf5 write routine, but i cannot say more than this.
antonio cervone
On Mon, Dec 24, 2012 at 9:55 PM, Villa Andrea (RSE)
<Andrea.Villa at rse-web.it> wrote:
> I'm using Trilinos 11.0.3, Hdf5 1.8.9
> All the HDF5 tests of trillinos have been passed, all the examples work
> fine.
> The code I've mailed work with 1,2,3 cores but fails with 4 cores.
>
>
>
>
> -----Messaggio originale-----
> Da: Antonio Cervone [mailto:ant.cervone at gmail.com]
> Inviato: sab 22/12/2012 10.46
> A: Villa Andrea (RSE)
> Cc: trilinos-users at software.sandia.gov
> Oggetto: Re: [Trilinos-Users] HDF5 - segmentation fault
>
> hi Andrea,
> i tested your example and it is working for me, so the problem is in
> the configuration/installation of your trilinos and hdf5 libraries.
> you can try turning on epetraext examples and tests to see if they are
> working.
> i used trilinos 10.12.2 and hdf5 1.8.9.
> ciao
>
> antonio
>
> On Sat, Dec 22, 2012 at 10:06 AM, Villa Andrea (RSE)
> <Andrea.Villa at rse-web.it> wrote:
>> I'm experiencing a segmentation fault running the following code with 4
>> processors.
>> I attach the driver below. The problem seems to be at line:
>> hdf5.Write("nodes",nodes_epetra);
>> Am I missing something?
>> Thankyou very much for any suggestion!
>>
>>
>>
>> #include <cmath>
>> #include <iostream>
>>
>> #include "Epetra_MpiComm.h"
>> #include "Epetra_Map.h"
>> #include "EpetraExt_DistArray.h"
>> #include "EpetraExt_HDF5.h"
>>
>>
>> int main(int argc, char *argv[])
>> {
>> MPI_Init(&argc,&argv);
>> Epetra_MpiComm epetraComm(MPI_COMM_WORLD);
>> int numMyElements;
>> int MyGlobalElements[4];
>>
>> if(epetraComm.MyPID() == 0)
>> {
>> numMyElements = 4;
>> MyGlobalElements[0] = 0;
>> MyGlobalElements[1] = 1;
>> MyGlobalElements[2] = 2;
>> MyGlobalElements[3] = 3;
>> }
>>
>> if(epetraComm.MyPID() == 1)
>> {
>> numMyElements = 4;
>> MyGlobalElements[0] = 4;
>> MyGlobalElements[1] = 5;
>> MyGlobalElements[2] = 6;
>> MyGlobalElements[3] = 7;
>> }
>>
>> if(epetraComm.MyPID() == 2)
>> {
>> numMyElements = 4;
>> MyGlobalElements[0] = 8;
>> MyGlobalElements[1] = 9;
>> MyGlobalElements[2] = 10;
>> MyGlobalElements[3] = 11;
>> }
>>
>> if(epetraComm.MyPID() == 3)
>> {
>> numMyElements = 2;
>> MyGlobalElements[0] = 12;
>> MyGlobalElements[1] = 13;
>> }
>>
>> Epetra_Map mappa(-1,numMyElements,MyGlobalElements,0,epetraComm);
>> EpetraExt::DistArray<double> nodes_epetra(mappa,3);
>>
>> EpetraExt::HDF5 hdf5(epetraComm);
>> hdf5.Create("err.h5");
>> hdf5.Write("nodes",nodes_epetra);
>> hdf5.Close();
>>
>> MPI_Finalize();
>> }
>>
>>
>> RSE SpA ha adottato il Modello Organizzativo ai sensi del D.Lgs.231/2001,
>> in
>> forza del quale l'assunzione di obbligazioni da parte della Società
>> avviene
>> con firma di un procuratore, munito di idonei poteri. RSE adopts a
>> Compliance Programme under the Italian Law (D.Lgs.231/2001). According to
>> this RSE Compliance Programme, any commitment of RSE is taken by the
>> signature of one Representative granted by a proper Power of Attorney.
>>
>> Le informazioni contenute in questo messaggio di posta elettronica sono
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>> o
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>
>
> RSE SpA ha adottato il Modello Organizzativo ai sensi del D.Lgs.231/2001, in
> forza del quale l'assunzione di obbligazioni da parte della Società avviene
> con firma di un procuratore, munito di idonei poteri. RSE adopts a
> Compliance Programme under the Italian Law (D.Lgs.231/2001). According to
> this RSE Compliance Programme, any commitment of RSE is taken by the
> signature of one Representative granted by a proper Power of Attorney.
>
> Le informazioni contenute in questo messaggio di posta elettronica sono
> riservate e confidenziali e ne e' vietata la diffusione in qualsiasi modo o
> forma. Qualora Lei non fosse la persona destinataria del presente messaggio,
> La invitiamo a non diffonderlo e ad eliminarlo, dandone gentilmente
> comunicazione al mittente. The information included in this e-mail and any
> attachments are confidential and may also be privileged. If you are not the
> correct recipient, you are kindly requested to notify the sender
> immediately, to cancel it and not to disclose the contents to any other
> person.
RSE SpA ha adottato il Modello Organizzativo ai sensi del D.Lgs.231/2001, in forza del quale l'assunzione di obbligazioni da parte della Società avviene con firma di un procuratore, munito di idonei poteri.
RSE adopts a Compliance Programme under the Italian Law (D.Lgs.231/2001). According to this RSE Compliance Programme, any commitment of RSE is taken by the signature of one Representative granted by a proper Power of Attorney. Le informazioni contenute in questo messaggio di posta elettronica sono riservate e confidenziali e ne e' vietata la diffusione in qualsiasi modo o forma. Qualora Lei non fosse la persona destinataria del presente messaggio, La invitiamo a non diffonderlo e ad eliminarlo, dandone gentilmente comunicazione al mittente. The information included in this e-mail and any attachments are confidential and may also be privileged. If you are not the correct recipient, you are kindly requested to notify the sender immediately, to cancel it and not to disclose the contents to any other person.
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