On 10/18/2014 04:39 AM, Samrat Rao wrote:
Hi Rob & Ed,
I think that the machine i am using is not that bad. It was commissioned
in '12. Some basic info:
Performance
360 TFLOPS Peak & 304 TFLOPS sustained on LINPACK
Hardware
HP blade system C7000 with BL460c Gen8 blades
1088 nodes with 300 GB disk/node (319 TB)
2,176 Intel Xeon E5 2670 processors@ 2.6 GHz
17,408 processor cores, 68 TB main memory
FDR Infiniband based fully non-blocking fat-tree topology
2 PB high performance storage with lustre parallel file system
OK,then let's work up the software stack.
You've got a lustre file system, so you're going to need a halfway
decent MPI-IO implementation. good news: OpenMPI, MPICH, and MVAPICH all
have good lustre drivers. Please ensure you are running something
close to the latest version. (sometimes we find users -- somehow --
running ten year old MPICH code)
You need a recent-ish HDF5 library to make full use of the MPI-IO library.
You need the very latest netcdf library for assorted bug fixes (and
compatibility with the latest HDF5 library)
Debugging this stack over the mailing list is a bit of a challenge.
==rob
----
Using netCDF configured for parallel applications, i did manage to write
data on a single netCDF file using 512 procs --- but this was when i
reduced the grid nodes per proc to about 20-30. When i made the grid
nodes to about 100 i got this error too:
NetCDF: HDF error
----
There is another issue i need to share --- while compiling netCDF4 for
parallel usage, i had encountered errors during 'make check' in these
files: run_par_test.sh, run_f77_par_test.sh and run_f90_par_test.sh
These were related to mpiexec commands --- mpd.hosts issue. These errors
did not occur when i compiled netcdf for parallel on my desktop.
----
Dumping outputs from each processor gave me these errors --- it is not
that all such errors appear together - they are a bit random.
proxy:0:13@cn0083] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:73): one of the processes
terminated badly; aborting
[proxy:0:13@cn0083] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting
for completion
[proxy:0:13@cn0083] HYD_pmci_wait_for_childs_completion
(./pm/pmiserv/pmip_utils.c:1476): bootstrap server returned error
waiting for completion
[proxy:0:13@cn0083] main (./pm/pmiserv/pmip.c:392): error waiting for
event children completion
[mpiexec@cn0002] control_cb (./pm/pmiserv/pmiserv_cb.c:674): assert
(!closed) failed
[mpiexec@cn0002] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[mpiexec@cn0002] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:388): error waiting for event
[mpiexec@cn0002] main (./ui/mpich/mpiexec.c:718): process manager error
waiting for completion
cn0137:b279:beba2700: 132021042 us(132021042 us!!!): ACCEPT_RTU: rcv
ERR, rcnt=0 op=1 <- 10.1.1.136
cn1068:48c5:4b280700: 132013538 us(132013538 us!!!): ACCEPT_RTU: rcv
ERR, rcnt=-1 op=1 <- 10.1.5.47
cn1075:dba3:f8d7700: 132099675 us(132099675 us!!!): CONN_REQUEST:
SOCKOPT ERR Connection refused -> 10.1.1.51 16193 - RETRYING... 5
cn1075:dba3:f8d7700: 132099826 us(151 us): CONN_REQUEST: SOCKOPT ERR
Connection refused -> 10.1.1.51 16193 - RETRYING...4
cn1075:dba3:f8d7700: 132099942 us(116 us): CONN_REQUEST: SOCKOPT ERR
Connection refused -> 10.1.1.51 16193 - RETRYING...3
cn1075:dba3:f8d7700: 132100049 us(107 us): CONN_REQUEST: SOCKOPT ERR
Connection refused -> 10.1.1.51 16193 - RETRYING...2
cn1075:dba3:f8d7700: 132100155 us(106 us): CONN_REQUEST: SOCKOPT ERR
Connection refused -> 10.1.1.51 16193 - RETRYING...1
cn1075:dba3:f8d7700: 132100172 us(17 us): dapl_evd_conn_cb() unknown
event 0x0
----
Rob, I guess i will need to look into the io methods you listed.
Thanks for your time,
Samrat.
On Fri, Oct 17, 2014 at 10:00 PM, Rob Latham <robl@xxxxxxxxxxx
<mailto:robl@xxxxxxxxxxx>> wrote:
On 10/17/2014 11:25 AM, Ed Hartnett wrote:
Unless things have changed since my day, it is possible to read
pnetcdf
files with the netCDF library. It must be built with
--enable-pnetcdf
and with-pnetcdf=/some/location, IIRC.
Ed!
In this case, Samrat Rao was using pnetcdf to create CDF-5 (giant
variable) formatted files. To refresh your memory, Argonne and
Northwestern developed this file format with UCARS's signoff, with
the understanding that we (ANL and NWU) would never expect UCAR to
add support for it unless we did the work. I took a stab at it a
few years back and Wei-keng is taking a second crack at it right now.
the classic file formats CDF-1 and CDF-2 are fully inter-operable
between pnetcdf and netcdf.
==rob
On Fri, Oct 17, 2014 at 6:33 AM, Samrat Rao
<samrat.rao@xxxxxxxxx <mailto:samrat.rao@xxxxxxxxx>
<mailto:samrat.rao@xxxxxxxxx <mailto:samrat.rao@xxxxxxxxx>>> wrote:
Hi,
I'm sorry for the late reply.
I have no classic/netcdf-3 datasets --- datasets are to be
generated. All my codes are also new.
Initially i tried with pnetcdf, wrote a few variables, but
found
that the format was CDF-5 which 'normal' netcdf would not read.
I also need to read some bits of netcdf data in Matlab, so
i thought
of sticking to the usual netcdf-4 compiled for parallel io.
It is
also likely that i will have to share my workload with
others in my
group and/or leave the code for future people to work on.
Does matlab read cdf-5 files?
So i preferred the usual netcdf. Rob, i hope you are not
annoyed.
But most of the above is for another day. Currently i am stuck
elsewhere.
With a less no of processors, 216, the single netcdf file gets
created (i create i single netcdf file for each variable),
but for
anything above that i get these errors:
NetCDF: Bad chunk sizes.
Not sure where these errors come from.
Then i shifted to dumping outputs from each processor in simple
binary --- this works till about 1500 processors. Above
this number
the code gets stuck and eventually aborts.
This issue is not new. My colleague too had problems with
running
his code on 1500+ procs.
Today i came to know that opening a large number of files
(each proc
writes 1 file) can overwhelm the system --- solving this
requires
more than rudimentary techniques of writing --- or
understanding the
system's inherent parameters/bottlenecks.
So netcdf is probably out of bounds for now --- will try
again if
the simple binary write from each processor gets sorted out.
Does anyone have any suggestion?
Thanks,
Samrat.
On Thu, Oct 2, 2014 at 7:52 PM, Rob Latham
<robl@xxxxxxxxxxx <mailto:robl@xxxxxxxxxxx>
<mailto:robl@xxxxxxxxxxx <mailto:robl@xxxxxxxxxxx>>> wrote:
On 10/02/2014 01:24 AM, Samrat Rao wrote:
Thanks for your replies.
I estimate that i will be requiring approx 4000
processors
and a total
grid resolution of 2.5 billion for my F90 code. So
i need to
think/understand which is better - parallel netCDF
or the
'normal' one.
There are a few specific nifty features in pnetcdf that
can let
you get really good performance, but 'normal' netCDF is
a fine
choice, too.
Right now I do not know how to use parallel-netCDF.
It's almost as simple as replacing every 'nf' call with
'nfmpi'
but you will be just fine if you stick with UCAR netCDF-4
Secondly, i hope that the netCDF-4 files created by
either
parallel
netCDF or the 'normal' one are mutually compatible. For
analysis I will
be extracting data using the usual netCDF library,
so in
case i use
parallel-netCDF then there should be no
inter-compatibility
issues.
For truly large variables, parallel-netcdf introduced,
with some
consultation from the UCAR folks, a 'CDF-5' file
format. You
have to request it explicitly, and then in that one
case you
would have a pnetcdf file that netcdf tools would not
understand.
In all other cases, we work hard to keep pnetcdf and
"classic"
netcdf compatible. UCAR NetCDF has the option for an
HDF5-based
backend -- and in fact it's not an option if you want
parallel
I/O with NetCDF-4 -- is not compatible with
parallel-netcdf. By
now, your analysis tools surely are updated to
understand the
new HDF5-based backend?
I suppose it's possible you've got some 6 year old
analysis tool
that does not understand NetCDF-4's HDF5-based file format.
Parallel-netcdf would allow you to simulate with
parallel i/o
and produce a classic netCDF file. But I would be
shocked and a
little bit angry if that was actually a good reason to use
parallel-netcdf in 2014.
==rob
--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA
--
Samrat Rao
Research Associate
Engineering Mechanics Unit
Jawaharlal Centre for Advanced Scientific Research
Bangalore - 560064, India
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--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA
--
Samrat Rao
Research Associate
Engineering Mechanics Unit
Jawaharlal Centre for Advanced Scientific Research
Bangalore - 560064, India
--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA
