[Wrf-users] Unpredictable crashes - MPI/RSL/Nest related?(Scott)

Bart Brashers bbrashers at Environcorp.com
Fri Aug 26 12:18:24 MDT 2011

I have been running _almost_ the same setup as you, just using 

- GFS (and NAM 12km) GRIB files for inits
- WRFv3.3
- Openmpi-1.4.3
- PGI 10.6-0
- CentOS 5.x (2.6.18-53.1.14 kernel) on a Rocks 5.0 system
- gE interconnect.

I've not seen any similar problems.  FWIW, here's how I compiled stuff:

# grep -A11 DMPARALLEL /usr/local/src/wrf/WRFV3.3-openmpi/configure.wrf
DMPARALLEL      =        1
OMPCPP          =       # -D_OPENMP
OMP             =       # -mp -Minfo=mp -Mrecursive
OMPCC           =       # -mp
SFC             =       pgf90
SCC             =       gcc
CCOMP           =       pgcc
DM_FC           =       /usr/local/src/openmpi-1.4.3/bin/mpif90 
DM_CC           =       /usr/local/src/openmpi-1.4.3/bin/mpicc
FC              =        $(DM_FC)
CC              =       $(DM_CC) -DFSEEKO64_OK 
LD              =       $(FC)

# cat /usr/local/src/openmpi-1.4.3/my.configure
#!/bin/tcsh -f
setenv CC pgcc
setenv CFLAGS ''
setenv CXX pgCC
setenv CXXFLAGS ''
setenv FC pgf90
setenv FCFLAGS '-fast'
setenv FFLAGS '-O2'
setenv F90 pgf90
./configure --prefix=/usr/local/src/openmpi-1.4.3 --with-tm=/opt/torque
--disable-ipv6 >&! my.configure.out
make all >&! make.out
make install >&! make.install.out

Maybe there's something there that is different, that will help.


> -----Original Message-----
> From: wrf-users-bounces at ucar.edu [mailto:wrf-users-bounces at ucar.edu]
> Behalf Of Creighton, Glenn A Civ USAF AFWA 16 WS/WXN
> Sent: Thursday, August 25, 2011 12:57 PM
> To: wrf-users at ucar.edu
> Subject: Re: [Wrf-users] Unpredictable crashes - MPI/RSL/Nest
> related?(Scott)
> Scott,
> I have a similar problem with version 3.3, but not version 3.2.  It
may be a
> related issue to that which you are experiencing.  WRF will either seg
> somewhere in a call to alloc_space_field, or collect_on_comm,
> shows me that in these cases its dying in the MPI code ( calling
> -> libopen-pal.so.0 -> mca_btl_openib.so ).  It seems to die in a
> place every time.  Sometimes it will just hang while creating the
> wrfout file for d02.  It dies more frequently with nested runs.
> openmpi 1.4.2.
> I can run it 5 times and it will die 4 different ways.
> 1. module_comm_dm.f90:812 -> c_code.c:627 -> libmpi.so.0:?? ->
> pal.so.0:?? -> mca_btl_openib.so:?? libmlx4-rdav2.so:??
> 2. module_comm_nesting_dm:11793 -> c_code.c:627 -> libmpi.so.0:?? ->
> libopen-pal.so.0:?? -> mca_btl_openib.so:?? libmlx4-rdav2.so:?? ->
> libpthread.so.0:??
> 3. Hung writing wrfout_d02
> 4. mediation_integrate.f90:234 -> wrf_ext_read_field.f90:130 ->
> module_io.f90:14873 -> module_io.f90:15043 -> module_io.f90:16177 ...
-> ...
> -> libpthread.so.0:??
> I'm trying to work with the folks at ncar on this right now. It's a
> bug that seems very machine/compiler dependent (I'm running this on a
> with the ifort/icc also.  Same code works just fine on our AIX and
> Linux box we have here.  Very strange bug.
> Glenn
> -----Original Message-----
> Date: Wed, 24 Aug 2011 17:22:55 +0200
> From: Scott <scott.rowe at globocean.fr>
> Subject: [Wrf-users] Unpredictable crashes - MPI/RSL/Nest related?
> To: wrf-users at ucar.edu
> Message-ID: <4E55174F.9030306 at globocean.fr>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Hello all,
> I would like to know if others have come across this problem. The best
> can do is give a general description because it is quite
> In point form:
> - General Details -
> o I am performing a simulation with one parent domain (@25km) and
> child domains (@12.5km)
> o I am able to run just the parent domain without problem on 2 CPUs
> 4 cores each, ie 8 threads using MPI for communications, in a single
> computer.
> o I can run the parent domain on at least 30 odd cores without
> using MPI over a network. --> no nests, no worries
> o When I increase maxdom to include from one to three child domains,
> simulations will work fine when run on a single core. --> no MPI, no
> o As soon as I increase the number of cores, simulation success
> less likely. --> nests + MPI = worries
> o The strange thing is, when it performs correctly with say, two
> I will increase this to three cores, WRF will crash. Upon returning to
> two cores, this simulation will no longer function, and this without
> touching any other configuration aspect! Success is highly
> o When WRF crashes, it is most often in radiation routines, but
> sometimes in cumulus, this is also highly unpredictable.
> o Successive runs always crash at the same timestep and in the same
> o Timestep values for the parent domain and child domains are very
> conservative, and are also shown to function well when run without MPI
> will add
> o Many combinations of physics and dynamics options have been trialled
> to no avail. I note again that the options chosen, when run without
> run fine.
> o I have tried several configurations for the widths of relaxation
> for boundary conditions, a wider relaxation does seem to increase the
> chance of success, but this is hard to verify.
> o No CFL warnings appear in the rsl log files, the crashes are brusque
> and take the form of a segmentation fault whilst treating a child
> domain, never in the parent domain.
> o The only hint I have seen in output files is the TSK field becoming
> NaN over land inside the child domain. This does not occur 100% of the
> time however.
> It would thus appear to be a MPI or compiler issue rather than WRF.
> said, it is only the combination of nests AND MPI that causes
> not one or the other alone. Could it be RSL?
> Does anyone have any debugging ideas, even just general approaches to
> try and find the culprit?
> Any MPI parameters that could be ajusted?
> - Technical Details -
> o Using OpenMPI 1.4.3
> o Aiming for WRFV3.3 use but have tried v3.2.1 also
> o EM/ARW core
> o Compiler is ifort and icc v10.1
> o Have tried compiling with -O0, -O2 and -O3 with thourough cleaning
> each time
> o GFS boundary conditions, WPSV3.3. No obvious problems to report
> geo*.nc and met_em* appear fine.
> Thank you for any help you may be able to give.

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