The ABINIT Users Mailing List ( CLOSED )

[Chao Cao <cao@qtp.ufl.edu>]

There are definitely more places to change...:) I got the following 
error after doing the modifications mentioned here:

forrtl: severe (37): inconsistent record length, unit 26, file 
/scratch/ufhpc/ccao/test/t88/fort.26
mpirun noticed that job rank 2 with PID 10384 on node "r4a-s16.local" 
exited on signal 13.
[r4a-s35.local:30975] [0,0,1]-[0,0,0] mca_oob_tcp_msg_recv: readv failed 
with errno=104


And I'm still looking for the responsible part of the code... I am not 
familiar with abinit source code though, so it'll take long time... :p


Chao Cao

Matteo Giantomassi wrote:
> On Wed, 9 May 2007, Chao Cao wrote:
>
> > Dear abinit users:
> > I compiled latest abinit (version 5.3.4, 5.2.4 was also tried) with 
> > mpi parallel support. It was compiled with pathscale compiler/ACML 
> > library/Open MPI 1.1.4. Everything compiled OK and all the sequential 
> > tests were passed. Parallel execution of abinit (abinip) for ground 
> > state calculations were also performed without error. However, when I 
> > test on GW calculations, the code would always stop with errors.
> > For example, when I perform test_v4 t88, the code will stop after it 
> > goes into data set 2. In the log file (redirected from standard 
> > output), it stops at:
> > ......
> > ......
> >
> > End the ECHO of the ABINIT file header
> > =============================================================================== 
> >
> > Results from ABINIT code
> > Ab-initio plane waves calculation
> > Results from ABINIT code                     Ab-initio plane waves 
> > calculation                                              number of 
> > electrons 8
> > number of symmetries without inversion       24
> > number of bands                              30
> > number of plane waves                        89
> > ......
> > ......
> >  vkbsign:  1.0 1.0 0.0
> >
> >
> > k       eigenvalues [eV]
> > 1         -6.16   5.85   5.85   5.85   8.37   8.37   8.37   8.97  
> > 13.42 13.85
> >
> > 2         -5.35   1.88   5.07   5.07   7.73   9.34   9.34  12.53  
> > 13.18 13.18
> >
> > 3         -3.79  -1.20   4.62   4.62   7.26   9.19   9.19  13.33  
> > 16.71 16.71
> >
> > 4         -5.07   2.33   3.91   3.91   6.90   8.90  11.60  11.60  
> > 13.71 15.07
> >
> > 5         -3.42  -0.57   2.24   3.60   7.28  10.25  11.49  11.78  
> > 15.93 16.53
> >
> > 6         -4.10   0.33   2.02   4.49   8.21  10.60  10.92  11.81  
> > 12.40 15.39
> >
> > 7         -2.00  -2.00   2.94   2.94   6.46   6.46  15.78  15.78  
> > 17.07 17.07
> >
> > 8         -1.84  -1.84   1.91   1.91  10.09  10.09  10.74  10.74  
> > 16.42 16.42
> >
> > 3 additional processes aborted (not shown)
> > **********************************END OF LOG 
> > FILE************************************
> >
> >
> > and in the mpi.out:
> >
> >
> > lib-4091 : UNRECOVERABLE library error
> > A WRITE operation was attempted on a file with no write permission.
> >
> > Encountered during a sequential formatted WRITE to unit 7
> > Fortran unit 7 is connected to a sequential formatted text file: 
> > "fort.7"
> > Current format: (i3,7x,10f7.2/50(10x,10f7.2/))
> >               ^
> > Signal:6 info.si_errno:0(Success) si_code:-6()
> > [0] func:/opt/psc/ompi/1.1.4/lib/libopal.so.0 [0x2a959ab02b]
> > *** End of error message ***
> >
> >
> >
> > It looks to me that somewhere in the GW code, two or more MPI threads 
> > was trying to write to file "fort.7", and thus failed. Has anyone 
> > else encountered problem like this? Any suggestions would be 
> > appreciated.
> Hi,
>
> I think the problem is located in the src/15gw/rdkss.F90 subroutine at 
> line 463 (abinit version 5.3.4)
>
>  if (nsppol==2) then
>   write(6,'(i3,a,10f7.2/50(10x,10f7.2/))') ik,stag(isppol), 
> (Ha_eV*en(ik,ib,isppol),ib=min_band_proc,max_band_proc)
>   write(ab_out,'(i3,a,10f7.2/50(10x,10f7.2/))') ik,stag(isppol), 
> (Ha_eV*en(ik,ib,isppol),ib=min_band_proc,max_band_proc)
>  else
>   write(6,'(i3,7x,10f7.2/50(10x,10f7.2/))') ik, 
> (Ha_eV*en(ik,ib,isppol),ib=min_band_proc,max_band_proc)
>   write(ab_out,'(i3,7x,10f7.2/50(10x,10f7.2/))') ik, 
> (Ha_eV*en(ik,ib,isppol),ib=min_band_proc,max_band_proc)
>  end if
>
> As you said each processor/thread is trying to write on the main 
> output file and this causes the crash of the parallel run. You can 
> simply prevent all the other processors from writing on the main 
> output file by just adding the following statement
>
> if (me==0) then
>
>  if (nsppol==2) then
>   write(6,'(i3,a,10f7.2/50(10x,10f7.2/))') ik,stag(isppol), 
> (Ha_eV*en(ik,ib,isppol),ib=min_band_proc,max_band_proc)
>   write(ab_out,'(i3,a,10f7.2/50(10x,10f7.2/))') ik,stag(isppol), 
> (Ha_eV*en(ik,ib,isppol),ib=min_band_proc,max_band_proc)
>  else
>   write(6,'(i3,7x,10f7.2/50(10x,10f7.2/))') ik, 
> (Ha_eV*en(ik,ib,isppol),ib=min_band_proc,max_band_proc)
>   write(ab_out,'(i3,7x,10f7.2/50(10x,10f7.2/))') ik, 
> (Ha_eV*en(ik,ib,isppol),ib=min_band_proc,max_band_proc)
>  end if
>
> end if !of me==0
>
>
> The same if statement must be inserted at line 514 of the same 
> subroutine (rdkss)
>
> Moreover it's safe to change line 1195 of 21drive/sigma.F90 as follows :
>
> <OLD VERSION>
> call write_sigma_results(sp,sr,ikcalc,ikibz,en)
>
> <NEW VERSION> if (me==0) call write_sigma_results(sp,sr,ikcalc,ikibz,en)
>
>
> Maybe there are other parts of the code where each processors is trying
> to write on the main output file. We fixed such problems but you have 
> to wait for the next release.
> For the moment try to run the automatic tests in parallel, and let us 
> known if you encounter other problems.
>
> Hope this helps,
> Best Regards,
> Matteo Giantomassi
>
> > Best,
> >
> >
> >
> > Chao Cao
> >
> > Quantum Theory Project,
> > University of Florida
> > Gainesville, FL 32608