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]>>
> 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]>
>>>>> 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]>
>>> 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>
> *------------------------------------------------*
>
--
***
Sébastien Boisvert
http://boisvert.info
Sent from a PC (Linux panic 3.6.2-4.fc17.x86_64).
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