Hello,
You should CC the mailing list as I am sure that numerous people in
the genomics community would be interested by plant genome de novo assembly !
People at McGill University did some work on plant genomes with Ray too.
They posted their results on the list I think.
So you have something like 1 500 000 000 sequences, right ?
On what kind of hardware are you running ?
What's the latency reported in NetworkTest.txt ?
--
Sent from my IBM Blue Gene/Q
Sébastien
On 11/01/2012 12:57 PM, Christina Boucher wrote:
> Thanks. I ended up attaching the .openmpi-setup file in my top-level home
> directory and then adding the following line to my .bashrc: source
> ~/.openmpi-setup
>
> After recompiling it seems to be running on my Arabidopsis data. I am trying
> it with all 4 lanes and hoping that it works. I don't necessarily care if I
> get the *best* assembly but an assembly would be nice. Other assemblers have
> been bailing on memory with my 512G server but I am hopeful about your
> program.
>
> Thanks.
>
> Best,
> Christina
>
>
>
>
>
> On 2012-10-31, at 3:28 PM, Sébastien Boisvert <[email protected]
> <mailto:[email protected]>> wrote:
>
>> Hello,
>>
>> On 10/31/2012 03:48 PM, Christina Boucher wrote:
>>> MPI is already installed on my server… see:
>>> oak # rpm -qa | grep openmpi
>>> openmpi-devel-1.5.4-5.fc17.1.x86_64
>>> openmpi-1.5.4-5.fc17.1.x86_64
>>>
>>
>> This is something specific to Fedora 17 (which I happen to be using on my
>> laptop).
>> My answer below is not really related to Ray, but more related to Fedora 17.
>>
>> $ repoquery --list openmpi-1.5.4-5.fc17.1.x86_64 | grep mpiexec$ |grep bin
>> /usr/lib64/openmpi/bin/mpiexec
>>
>> $ repoquery --list openmpi-devel-1.5.4-5.fc17.1.x86_64 | grep mpicxx$ | grep
>> bin
>> /usr/lib64/openmpi/bin/mpicxx
>>
>>
>> However, the default PATH for a user on Fedora 17 is:
>>
>> [test@panic ~]$ echo $PATH
>> /usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/home/test/.local/bin:/home/test/bin
>>
>>
>> You can fix this in Fedora 17 by adding the following 2 lines to your
>> $HOME/.bashrc:
>>
>> export PATH=/usr/lib64/openmpi/bin:$PATH
>> export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib/:$LD_LIBRARY_PATH
>>
>>
>> Let me know if that work for you.
>>
>>
>> Sébastien
>>
>>> oak # rpm -qa | grep openmpi
>>> openmpi-devel-1.5.4-5.fc17.1.x86_64
>>> openmpi-1.5.4-5.fc17.1.x86_64
>>>
>>> Still the installation problems persist….
>>>
>>> Christina
>>>
>>>
>>>
>>> On 2012-10-31, at 11:26 AM, Sébastien Boisvert
>>> <[email protected] <mailto:[email protected]>
>>> <mailto:[email protected]>> wrote:
>>>
>>>> Hello,
>>>>
>>>>> make[1]: mpicxx: Command not found
>>>>
>>>> To install Ray, you need an MPI library. You don't have one installed.
>>>>
>>>> For example, on Fedora, the packages are openmpi, openmpi-devel, gcc-c++.
>>>>
>>>>> In addition, is the the max kmer length 32? Most people are using upwards
>>>>> to 55….?
>>>>
>>>> The maximum k-mer length is set at compilation. The default is
>>>> MAXKMERLENGTH=32.
>>>> To change that:
>>>>
>>>> make MAXKMERLENGTH=64
>>>>
>>>>
>>>> Sébastien
>>>>
>>>> On 10/31/2012 12:50 PM, Christina Boucher wrote:
>>>>>>>
>>>>>>> I am trying to use your Ray assembler. I've been using Spades (mainly
>>>>>>> because I am formerly
>>>>>>> from Pavel Pevzner's lab) but running out of memory on a large dataset.
>>>>>>
>>>>>> Maybe processing your large dataset is more amenable with a distributed
>>>>>> assembler.
>>>>>
>>>>> Spades group released a new version yesterday that's supposed to use less
>>>>> memory. I am trying that and the Ray assembler.
>>>>>
>>>>>
>>>>>> To get it and install it:
>>>>>>
>>>>>> $ wget
>>>>>> http://downloads.sourceforge.net/project/denovoassembler/Ray-v2.1.0.tar.bz2
>>>>>> $ sha1sum Ray-v2.1.0.tar.bz2
>>>>>> 4c09f2731445852857af53b65aa47e444792eeb0 Ray-v2.1.0.tar.bz2
>>>>>>
>>>>>> $ tar xjf Ray-v2.1.0.tar.bz2
>>>>>> $ cd Ray-v2.1.0/
>>>>>> $ make
>>>>>
>>>>>
>>>>> The problem is this compilation error: After those steps I get the
>>>>> following error:
>>>>>
>>>>> eggs:~/Ray-v2.1.0$ make
>>>>>
>>>>> Compilation options (you can change them of course)
>>>>>
>>>>> PREFIX = install-prefix
>>>>> MAXKMERLENGTH = 32
>>>>> FORCE_PACKING = n
>>>>> ASSERT = n
>>>>> HAVE_LIBZ = n
>>>>> HAVE_LIBBZ2 = n
>>>>> INTEL_COMPILER = n
>>>>> MPICXX = mpicxx
>>>>> GPROF = n
>>>>> OPTIMIZE = y
>>>>> DEBUG = n
>>>>>
>>>>> Compilation and linking flags (generated automatically)
>>>>>
>>>>> CXXFLAGS = -Wall -std=c++98 -O3 -D MAXKMERLENGTH=32 -D
>>>>> RAY_VERSION=\"2.1.0\"
>>>>> LDFLAGS =
>>>>>
>>>>> make[1]: Entering directory
>>>>> `/s/parsons/f/fac/cboucher/Ray-v2.1.0/RayPlatform'
>>>>> mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.1.0\"
>>>>> -D RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o memory/ReusableMemoryStore.o
>>>>> memory/ReusableMemoryStore.cpp
>>>>> make[1]: mpicxx: Command not found
>>>>> make[1]: *** [memory/ReusableMemoryStore.o] Error 127
>>>>> make[1]: Leaving directory
>>>>> `/s/parsons/f/fac/cboucher/Ray-v2.1.0/RayPlatform'
>>>>> make[1]: Entering directory `/s/parsons/f/fac/cboucher/Ray-v2.1.0/code'
>>>>> mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.1.0\"
>>>>> -I ../RayPlatform -I. -c -o application_core/ray_main.o
>>>>> application_core/ray_main.cpp
>>>>> make[1]: mpicxx: Command not found
>>>>> make[1]: *** [application_core/ray_main.o] Error 127
>>>>> make[1]: Leaving directory `/s/parsons/f/fac/cboucher/Ray-v2.1.0/code'
>>>>> mpicxx code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o Ray
>>>>> make: mpicxx: Command not found
>>>>> make: *** [Ray] Error 127
>>>>>
>>>>>
>>>>> Any thoughts?
>>>>>
>>>>> In addition, is the the max kmer length 32? Most people are using upwards
>>>>> to 55….?
>>>>>
>>>>> Christina
>>>>>
>>>>>
>>>>>>
>>>>>> $ mpiexec -n 1 ./Ray -version
>>>>>> $ mpiexec -n 999 ./Ray -k 31 -p 1.left.fastq 1.right.fastq -p
>>>>>> 2.left.fastq 2.right.fastq -o Test
>>>>>>
>>>>>>> Best,
>>>>>>> Christina
>>>>>>>
>>>>>>> *
>>>>>>> ------------------------------------------------*
>>>>>>> *Christina Boucher*
>>>>>>> **Department of Computer Science
>>>>>>> Colorado State University
>>>>>>> Fort Collins, CO 80523
>>>>>>> +1.970.491.8063
>>>>>>> [email protected] <mailto:[email protected]>
>>>>>>> <mailto:[email protected]> <mailto:[email protected]>
>>>>>>> <mailto:[email protected]>
>>>>>>> www.christinaboucher.com <http://www.christinaboucher.com>
>>>>>>> <http://www.christinaboucher.com> <http://www.christinaboucher.com>
>>>>>>> <http://www.christinaboucher.com>
>>>>>>> *------------------------------------------------*
>>>>>>>
>>>>>>
>>>>>
>>>>> *
>>>>> ------------------------------------------------*
>>>>> *Christina Boucher*
>>>>> **Department of Computer Science
>>>>> Colorado State University
>>>>> Fort Collins, CO 80523
>>>>> +1.970.491.8063
>>>>> [email protected] <mailto:[email protected]>
>>>>> <mailto:[email protected]> <mailto:[email protected]>
>>>>> www.christinaboucher.com <http://www.christinaboucher.com>
>>>>> <http://www.christinaboucher.com> <http://www.christinaboucher.com>
>>>>> *------------------------------------------------*
>>>>>
>>>>
>>>>
>>>> --
>>>> ***
>>>> Sébastien Boisvert
>>>> http://boisvert.info
>>>> Sent from a PC (Linux panic 3.6.2-4.fc17.x86_64).
>>>
>>> *
>>> ------------------------------------------------*
>>> *Christina Boucher*
>>> **Department of Computer Science
>>> Colorado State University
>>> Fort Collins, CO 80523
>>> +1.970.491.8063
>>> [email protected] <mailto:[email protected]>
>>> <mailto:[email protected]>
>>> www.christinaboucher.com <http://www.christinaboucher.com>
>>> <http://www.christinaboucher.com>
>>> *------------------------------------------------*
>>>
>>
>>
>> --
>> ***
>> Sébastien Boisvert
>> http://boisvert.info
>> Sent from a PC (Linux panic 3.6.2-4.fc17.x86_64).
>
> *
> ------------------------------------------------*
> *Christina Boucher*
> **Department of Computer Science
> Colorado State University
> Fort Collins, CO 80523
> +1.970.491.8063
> [email protected] <mailto:[email protected]>
> www.christinaboucher.com <http://www.christinaboucher.com>
> *------------------------------------------------*
>
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