Perfect, that worked, thanks again!
Quite a big difference, with k=31 and de Bruijn routing it took 9 hours,
whereas k=41 without routing specified took 1:30h on a Cray XE6 system with
1024 cores and ~250M pairs.
Best regards,
Ino
From: ino.debru...@scilifelab.se
To: sebastien.boisver...@ulaval.ca
Date: Fri, 5 Apr 2013 12:32:42 +0200
CC: denovoassembler-users@lists.sourceforge.net
Subject: Re: [Denovoassembler-users] Long execution time, seems to be stuck at
Rank 0
Alright, I'll try that then, thank you!
> Date: Thu, 4 Apr 2013 20:23:13 -0400
> From: sebastien.boisver...@ulaval.ca
> To: ino.debru...@scilifelab.se
> CC: denovoassembler-users@lists.sourceforge.net
> Subject: Re: [Denovoassembler-users] Long execution time, seems to be stuck
> at Rank 0
>
> I think you should run Ray with a different value for
> -read-write-checkpoints just to rule out bad checkpoints . Maybe your
> checkpoints were
> generated with a different number of ranks.
>
> On 04/04/13 04:26 AM, Ino de Bruijn wrote:
> > Hi,
> >
> > Hypothesis 0. I have 249,559,758 pairs in total so it would seem Ray is
> > running on one MPI rank.
> >
> > Hypothesis 1. If I look at the SequencePartition.txt it seems the reads are
> > properly partitioned:
> >
> > $ head -2 metassemble/assemblies/ray/out_41/SequencePartition.txt
> > #Rank FirstSequence LastSequence NumberOfSequences
> > 0 0 243709 243710
> >
> > $ tail -1 metassemble/assemblies/ray/out_41/SequencePartition.txt
> > 1023 249315330 249559757 244428
> >
> > If I look at the log it also finds checkpoints for all different ranks. But
> > maybe it uses the old routing
> > I specified? Or is that not stored in the checkpoints?
> >
> > Best regards,
> > Ino
> >
> > > Date: Wed, 3 Apr 2013 11:10:27 -0400
> > > From: sebastien.boisver...@ulaval.ca
> > > To: ino.debru...@scilifelab.se
> > > CC: denovoassembler-users@lists.sourceforge.net
> > > Subject: Re: [Denovoassembler-users] Long execution time, seems to be
> > stuck at Rank 0
> > >
> > > Hello,
> > >
> > > On 02/04/13 04:37 AM, Ino de Bruijn wrote:
> > > > Dear Sébastien Biosvert,
> > > >
> > > > I tried a run without specifying the route-messages parameter but the
> > problem remains the same.
> > > >
> > > > At the end only Rank 0 is outputting data:
> > > >
> > > > Speed RAY_SLAVE_MODE_ADD_EDGES 4066 units/second
> > > > Estimated remaining time for this step: 12 hours, 36 minutes, 45
> > seconds
> > > > Rank 0 is adding edges [64950001/249559758]
> > >
> > > 249559758 is the number of reads for MPI rank 0. And you have 1024 such
> > MPI ranks.
> > >
> > > There are two alternative hypotheses:
> > >
> > > Hypothesis 0. You have 1024 * 249559758 = 255 549 192 192 reads, which
> > is a lot !
> > >
> > > Hypothesis 1: Ray is actually running on 1 MPI rank.
> > >
> > >
> > > You can check the facts to validate one of the hypothesis with this
> > command:
> > >
> > >
> > > cat out_41/SequencePartition.txt
> > >
> > >
> > >
> > > I think that the problem is that you are re-using old checkpoints that
> > were not generated with
> > > 1024 MPI ranks.
> > >
> > > >
> > > > The command I used was:
> > > >
> > > > mpiexec -n 1024 Ray \
> > > > -k \
> > > > 41 \
> > > > -i \
> > > > metassemble/assemblies/ray/pair.fastq \
> > > > -o \
> > > > metassemble/assemblies/ray/out_41 \
> > > > -read-write-checkpoints \
> > > > metassemble/assemblies/ray/out_41.cp
> > > >
> > > > on a Cray XE6 system:
> > http://www.pdc.kth.se/resources/computers/lindgren/hardware.
> > > >
> > > > Best regards,
> > > > Ino
> > > >
> > > >
> > > >
> > ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------!
> > > ---
> > > > From: ino...@hotmail.com
> > > > To: sebastien.boisver...@ulaval.ca
> > > > CC: denovoassembler-users@lists.sourceforge.net
> > > > Subject: RE: [Denovoassembler-users] Long execution time, seems to be
> > stuck at Rank 0
> > > > Date: Tue, 26 Mar 2013 00:26:05 +0100
> > > >
> > > >
> > > > Ah excellent! My knowledge of these kind of systems is clearly
> > lacking. Thanks a lot!
> > > >
> > > > Best regards,
> > > > Ino
> > > >
> > > > > Date: Mon, 25 Mar 2013 17:44:12 -0400
> > > > > From: sebastien.boisver...@ulaval.ca
> > > > > To: ino...@hotmail.com
> > > > > CC: denovoassembler-users@lists.sourceforge.net
> > > > > Subject: Re: [Denovoassembler-users] Long execution time, seems to
> > be stuck at Rank 0
> > > > >
> > > > > On 25/03/13 12:46 PM, Ino de Bruijn wrote:
> > > > > > Thanks a lot for the prompt reply!
> > > > > >
> > > > > > > What is your interconnect ?
> > > > > > >
> > > > > > > Do you have Infiniband ?
> > > > > >
> > > > > > It is a Cray XE6 system that uses the Cray Gemini interconnect
> > technology. These are the full specs:
> > http://www.pdc.kth.se/resources/computers/lindgren/hardware
> > > > >
> > > > > In that case, you don't need to route your messages !
> > > > >
> > > > > The Cray XE6 has the best interconnect out there ! It's a 5D torus.
> > > > >
> > > > > >
> > > > > > Is the polytope connection type good for this type of interconnect
> > as well?
> > > > > >
> > > > >
> > > > > You should remove the -route-messages option altogether.
> > > > >
> > > > >
> > > > > -route-messages is useful when using buggy Infiniband fabrics or TCP
> > networks. If you use something like:
> > > > >
> > > > > * Cray XE6
> > > > > * IBM Blue Gene/Q
> > > > > * Intel PSM (QLogic Infiniband)
> > > > > * IBM iDataPlex
> > > > >
> > > > >
> > > > > you don't need this option because these systems are really good and
> > provide low-latency any-to-any message passing.
> > > > >
> > > > >
> > > > > > Best regards,
> > > > > > Ino
> > > > > >
> > > > > > > Date: Mon, 25 Mar 2013 11:24:21 -0400
> > > > > > > From: sebastien.boisver...@ulaval.ca
> > > > > > > To: denovoassembler-users@lists.sourceforge.net
> > > > > > > Subject: Re: [Denovoassembler-users] Long execution time, seems
> > to be stuck at Rank 0
> > > > > > >
> > > > > > > On 25/03/13 05:32 AM, Ino de Bruijn wrote:
> > > > > > > > Dear Sébastien Boisvert,
> > > > > > > >
> > > > > > > > I am trying to assemble a paired-end Illumina Hiseq library of
> > about 1 billion reads. I ran Ray with:
> > > > > > > >
> > > > > > > > mpiexec -n 1024 Ray \
> > > > > > > > -k \
> > > > > > > > 31 \
> > > > > > > > -i \
> > > > > > > > metassemble/assemblies/ray/pair.fastq \
> > > > > > > > -o \
> > > > > > > > metassemble/assemblies/ray/out_31 \
> > > > > > > > -read-write-checkpoints \
> > > > > > > > metassemble/assemblies/ray/out_31.cp \
> > > > > > > > -route-messages
> > > > > > >
> > > > > > > Without other arguments, -route-messages will use a de Bruijn
> > graph for routing, which is not really good.
> > > > > > >
> > > > > > > What is your interconnect ?
> > > > > > >
> > > > > > > Do you have Infiniband ?
> > > > > > >
> > > > > > >
> > > > > > > Use this instead (the polytope is the best routing engine in
> > RayPlatform):
> > > > > > >
> > > > > > > -route-messages -connection-type polytope -routing-graph-degree
> > 62
> > > > > > >
> > > > > > > (from
> > https://github.com/sebhtml/ray/blob/master/Documentation/Routing.txt )
> > > > > > >
> > > > > > > >
> > > > > > > > For k=31 the assembly succeeds in ~9h on 1,024 cores. If I try
> > higher values of k (i.e. {41..81..10}), the run
> > > > > > > > is exited by the scheduler after a day (max run time is one
> > day). If I look at the log of the stdout it seems
> > > > > > > > like only Rank 0 is doing something at the end. Here are are a
> > couple of lines from the output:
> > > > > > > >
> > > > > > >
> > > > > > > Well, you are using a de Bruijn graph for routing your messages.
> > A de Bruijn graph is theoretically cool for routing messages,
> > > > > > > but in practice it's very bad because it's not adaptative and
> > it's just a pit containing so many choke points.
> > > > > > >
> > > > > > > From the manual
> > https://github.com/sebhtml/ray/blob/master/MANUAL_PAGE.txt :
> > > > > > >
> > > > > > > -connection-type type
> > > > > > > Sets the connection type for routes.
> > > > > > > Accepted values are debruijn, hypercube, polytope, group,
> > random, kautz and complete. Default is debruijn.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > > Rank 0 is counting k-mers in sequence reads
> > [51200001/249559758]
> > > > > > > > Speed RAY_SLAVE_MODE_ADD_VERTICES 4909 units/second
> > > > > > > > Estimated remaining time for this step: 11 hours, 13 minutes,
> > 27 seconds
> > > > > > > >
> > > > > > > > This keeps going while only Rank 0 is outputting. The final
> > message says there are 30 minutes left for k=41. For 51 and 61 it is around
> > 10-20h left and for k=71 and k=81 it is about an hour again.
> > > > > > >
> > > > > > > You should definitely use the polytope. It has no choke points,
> > and routes are adaptative (i.e. messages between A and B will use several
> > paths).
> > > > > > >
> > > > > > > > Does it only use Rank 0 at this step because this step can
> > only be done by one core or is the graph that Rank 0 contains highly
> > complex or something?
> > > > > > >
> > > > > > > At 1024 MPI ranks, rank 0 is one of the hubs in a de Bruijn
> > graph.
> > > > > > >
> > > > > > > >
> > > > > > > > If I want to continue running Ray. Can I resume the process by
> > running the same parameters, but using only one core (-n 1)? Or
> > > > > > > > should I use more cores?
> > > > > > >
> > > > > > > You have to re-launch Ray with the same command except the -o
> > parameter.
> > > > > > >
> > > > > > > Example:
> > > > > > >
> > > > > > > mpiexec -n 1024 Ray \
> > > > > > > -k \
> > > > > > > 31 \
> > > > > > > -i \
> > > > > > > metassemble/assemblies/ray/pair.fastq \
> > > > > > > -o \
> > > > > > > metassemble/assemblies/ray/out_31 \
> > > > > > > -read-write-checkpoints \
> > > > > > > metassemble/assemblies/ray/out_31.cp \
> > > > > > > -route-messages -connection-type polytope -routing-graph-degree
> > 62
> > > > > > >
> > > > > > >
> > > > > > > > When is the checkpointing done?
> > > > > > >
> > > > > > > At each step.
> > > > > > >
> > > > > > > To see your checkpoint files:
> > > > > > >
> > > > > > > ls metassemble/assemblies/ray/out_31.cp | less
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > >
> > > > > > > > It seems like I have to remove the output dir to resume from a
> > checkpoint. Is that correct?
> > > > > > >
> > > > > > > No. It's not necessary. You can instead provide a new output
> > directory.
> > > > > > >
> > > > > > > >
> > > > > > > > Best regards,
> > > > > > > > Ino de Bruijn
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
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