Re: [OMPI users] [version 2.1.5] invalid memory reference

2018-10-12 Thread Patrick Bégou
I have downloaded the nightly snapshot tarball of october 10th 2018 for the 3.1 version and it solves the memory problem. I ran my test case on 1, 2, 4, 10, 16, 20, 32, 40, and 64 cores successfully. This version also allows to compile my prerequisites libraries, so we can use it out of the box to

Re: [OMPI users] [version 2.1.5] invalid memory reference

2018-10-11 Thread Jeff Hammond
MPI_LB, MPI_UB and MPI_Type_struct have been deprecated since MPI-2 and were removed in MPI-3 ( https://www.mpi-forum.org/docs/mpi-3.1/mpi31-report/node34.htm). It is trivial to replace MPI_Type_struct with MPI_Type_create_struct. Replacing MPI_UB and MPI_LB with MPI_Type_create_resized but it

Re: [OMPI users] [version 2.1.5] invalid memory reference

2018-10-11 Thread Jeff Squyres (jsquyres) via users
Patrick -- You might want to update your HDF code to not use MPI_LB and MPI_UB -- these constants were deprecated in MPI-2.1 in 2009 (an equivalent function, MPI_TYPE_CREATE_RESIZED was added in MPI-2.0 in 1997), and were removed from the MPI-3.0 standard in 2012. Meaning: the death of these

Re: [OMPI users] [version 2.1.5] invalid memory reference

2018-10-11 Thread Nathan Hjelm via users
Those features (MPI_LB/MPI_UB/MPI_Type_struct) were removed in MPI-3.0. It is fairly straightforward to update the code to be MPI-3.0 compliant. MPI_Type_struct -> MPI_Type_create_struct MPI_LB/MPI_UB -> MPI_Type_create_resized Example: types[0] = MPI_LB; disp[0] = my_lb; lens[0] = 1;

Re: [OMPI users] [version 2.1.5] invalid memory reference

2018-10-11 Thread Patrick Begou
Hi Jeff and George thanks for your answer. I find some time to work again on this problem dans I have downloaded OpenMPI 4.0.0rc4. It compiles without any problem but building the first dependance of my code (hdf5 1.8.12) with this version 4 fails: ../../src/H5Smpio.c:355:28: error: 'MPI_LB'

Re: [OMPI users] [version 2.1.5] invalid memory reference

2018-09-19 Thread Jeff Squyres (jsquyres) via users
Yeah, it's a bit terrible, but we didn't reliably reproduce this problem for many months, either. :-\ As George noted, it's been ported to all the release branches but is not yet in an official release. Until an official release (4.0.0 just had an rc; it will be released soon, and 3.0.3 will

Re: [OMPI users] [version 2.1.5] invalid memory reference

2018-09-19 Thread George Bosilca
I can't speculate on why you did not notice the memory issue before, simply because for months we (the developers) didn't noticed and our testing infrastructure didn't catch this bug despite running millions of tests. The root cause of the bug was a memory ordering issue, and these are really

Re: [OMPI users] [version 2.1.5] invalid memory reference

2018-09-19 Thread Patrick Begou
Hi George thanks for your answer. I was previously using OpenMPI 3.1.2 and have also this problem. However, using --enable-debug --enable-mem-debugat configuration time, I was unable to reproduce the failure and it was quite difficult for me do trace the problem. May be I have not run enought

Re: [OMPI users] [version 2.1.5] invalid memory reference

2018-09-18 Thread George Bosilca
Few days ago we have pushed a fix in master for a strikingly similar issue. The patch will eventually make it in the 4.0 and 3.1 but not on the 2.x series. The best path forward will be to migrate to a more recent OMPI version. George. On Tue, Sep 18, 2018 at 3:50 AM Patrick Begou <

[OMPI users] [version 2.1.5] invalid memory reference

2018-09-18 Thread Patrick Begou
Hi I'm moving a large CFD code from Gcc 4.8.5/OpenMPI 1.7.3 to Gcc 7.3.0/OpenMPI 2.1.5 and with this latest config I have random segfaults. Same binary, same server, same number of processes (16), same parameters for the run. Sometimes it runs until the end, sometime I get  'invalid memory