netCDF problem with rev 14 : LFS support absent?
Posted: Thu Nov 11, 2010 9:21 am
Dear all,
I think I have focussed the problem of netcdf with rev 14. By increasing the number of k-points, files get larger and larger. I found this error during (actually at the end of) the setup run:
The problem occurs when YAMBO tries to store data on ndb.kindx. As long as such file keeps its dimension < 2Gb the problem does not occur, but when it becomes larger than 2GB, i.e. for very fine kgrids -> NetCDF error.
I put a lot of prints to analize the origin of the error and I found that YAMBO (rev14) correctly ends all loops required by the setup run without errors.
But when I tried to use tools provided by netcdf I discovered that:
which indicates that Large File support is absent, according to http://www.unidata.ucar.edu/software/ne ... 20Support5 .
Note that, instead, I compiled rev14 with --enable-largedb as you can see from this part of my config.log:
In order to go further, I put this prints in the criminal subroutine, i.e. src/modules/mod_IO.F
The result is of course that the optional flag is not present when io_connect is called, indeed if you look at src/io/ioQINDX.F, the io_connect subroutine is called without specific declaration of the logical ENABLE_LARGE_FILE
So, as far as I have understood, there is no correlation between the flag --enable-largedb and this part of the code. As a consequence I can run only simulations that lead to files < 2Gb, otherwise my simulations are stopped with such error.
Hope to have been clear and to be useful to let you resolve the problem.
Cheers!
Marco
I think I have focussed the problem of netcdf with rev 14. By increasing the number of k-points, files get larger and larger. I found this error during (actually at the end of) the setup run:
Code: Select all
<03h-20m-02s> SE indexes |############### | [075%] 05m-33s(E) 07m-24s(X)
<03h-20m-24s> SE indexes |################ | [080%] 05m-55s(E) 07m-24s(X)
<03h-20m-47s> SE indexes |################# | [085%] 06m-18s(E) 07m-25s(X)
<03h-21m-11s> SE indexes |################## | [090%] 06m-42s(E) 07m-26s(X)
<03h-21m-34s> SE indexes |################### | [095%] 07m-05s(E) 07m-27s(X)
<03h-21m-57s> SE indexes |####################| [100%] 07m-28s(E) 07m-28s(X)
[ERROR] STOP signal received while in :[03] Transferred momenta grid
[ERROR][NetCDF] NetCDF: One or more variable sizes violate format constraints
I put a lot of prints to analize the origin of the error and I found that YAMBO (rev14) correctly ends all loops required by the setup run without errors.
But when I tried to use tools provided by netcdf I discovered that:
Code: Select all
-bash-3.2$ ncdump -k ndb.kindx
classic
-bash-3.2$ od -An -c -N4 ndb.kindx
C D F 001
Note that, instead, I compiled rev14 with --enable-largedb as you can see from this part of my config.log:
Code: Select all
(...)
enable_debug='yes'
enable_dp='no'
enable_largedb='yes'
(...)
Code: Select all
(...)
#if defined _NETCDF_IO
!
! Setting NF90_64BIT_OFFSET causes netCDF to create a 64-bit
! offset format file, instead of a netCDF classic format file.
! The 64-bit offset format imposes far fewer restrictions on very large
! (i.e. over 2 GB) data files. See Large File Support.
!
! http://www.unidata.ucar.edu/software/netcdf/docs/netcdf/Large-File-Support.html
! http://www.unidata.ucar.edu/software/netcdf/faq-lfs.html
!
CREATE_MODE=nf90_share
if ( present(ENABLE_LARGE_FILE)) CREATE_MODE=ior(nf90_share,nf90_64bit_offset)
if ( present(ENABLE_LARGE_FILE)) then
print*,'present ENABLE_LARGE_FILE', ENABLE_LARGE_FILE, desc
else
print*, 'not present ENABLE_LARGE_FILE'
endif
!
if ( (io_action(ID)==OP_APP_WR_CL.or.io_action(ID)==OP_APP) ) then
!
if( file_exists(trim(io_file(ID))) ) then
call netcdf_call(nf90_open(trim(io_file(ID)),&
& ior(nf90_write,nf90_share),io_unit(ID)))
else
call netcdf_call(nf90_create(trim(io_file(ID)),CREATE_MODE,io_unit(ID)))
call netcdf_call(nf90_enddef(io_unit(ID)))
if (io_action(ID)==OP_APP_WR_CL) io_action(ID)=OP_WR_CL
if (io_action(ID)==OP_APP) io_action(ID)=OP_WR
endif
!
else
!
call netcdf_call(nf90_create(trim(io_file(ID)),CREATE_MODE,io_unit(ID)))
call netcdf_call(nf90_enddef(io_unit(ID)))
!
endif
#endif
(...)
Code: Select all
ioQINDX=io_connect(desc='kindx',type=1,ID=io_db)
Hope to have been clear and to be useful to let you resolve the problem.
Cheers!
Marco