[gentoo-cluster] eselect-mpi issues

[gentoo-cluster] eselect-mpi issues

[Bryan Green]

Hello,

I'm beginning to give empi/eselect-mpi a try.  Bravo, Justin, for making
these!

I've run into one bug in eselect-mpi that effects csh users (a popular
shell where I work).  There is simply one setenv line that has bash syntax
rather than csh syntax.  I already submitted a bug: its bug 226105.
Here is the patch to fix it:

================================================
--- files/mpi.eselect-0.0.3     (revision 1137)
+++ files/mpi.eselect-0.0.3     (working copy)
@@ -161,7 +161,7 @@
 setenv PATH "${binpath}"
  setenv MANPATH "${manpath}"
   setenv LD_LIBRARY_PATH "${lld}"
   -setenv ESELECT_MPI_IMP="${1}"
   +setenv ESELECT_MPI_IMP "${1}"
    EOF
     
          echo "Remember to source ${user_ev_sh} or ${user_ev_csh}"
================================================

Also, in the README file, the for loop in step 6 is incorrect:

for i in $(ls ${HOME}/.env.d/*); do
    source ${HOME}/.env.d/${i}
done

Results in:

-bash: /home/bgreen/.env.d//home/bgreen/.env.d/mpi.csh: No such file or directory
-bash: /home/bgreen/.env.d//home/bgreen/.env.d/mpi.sh: No such file or directory


On the system where I'm using empi, I've created files in /etc/profile.d to
source the user's .env.d files when they log in.  What do you think about
having the eselect-mpi ebuild install these, so mpi users dont have to do
that part manually?  They would instead just have to source /etc/profile or
/etc/csh.login after running 'eselect mpi'.


Here are my versions of the files in /etc/profile.d:

==============
mpi-config.sh
==============
if [ -d ${HOME}/.env.d ]; then
    for i in ${HOME}/.env.d/*.sh ; do
        . "${i}"
    done
    unset i
fi

==============
mpi-config.csh
==============
if ( -d ${HOME}/.env.d ) then
    set nonomatch
    foreach i ( ${HOME}/.env.d/*.csh )
        source ${i}
    end
    unset i nonomatch
endif

==============

-bryan

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gentoo-cluster@lists.gentoo.org mailing list

Re: [gentoo-cluster] eselect-mpi issues

[Bryan Green]

Bryan Green writes:
> They would instead just have to source /etc/profile or
> /etc/csh.login after running 'eselect mpi'.

Actually, the current instructions from 'eselect mpi' to "Remember to source
/root/.env.d/mpi.sh or /root/.env.d/mpi.csh" are sufficient.  It wouldn't
be necessary to source the global scripts after running 'eselect mpi'.

-bryan

-- 
gentoo-cluster@lists.gentoo.org mailing list

[gentoo-cluster] Re: eselect-mpi issues

[Justin Bronder]

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On 12/06/08 11:28 -0700, Bryan Green wrote:
> Hello,
> 
> I'm beginning to give empi/eselect-mpi a try.  Bravo, Justin, for making
> these!

Thanks for trying them out, I'm hoping someone else finds them as useful as I
have.

> 
> I've run into one bug in eselect-mpi that effects csh users (a popular
> shell where I work).  There is simply one setenv line that has bash syntax
> rather than csh syntax.  I already submitted a bug: its bug 226105.
> Here is the patch to fix it:
> 
> ================================================
> --- files/mpi.eselect-0.0.3     (revision 1137)
> +++ files/mpi.eselect-0.0.3     (working copy)
> @@ -161,7 +161,7 @@
>  setenv PATH "${binpath}"
>   setenv MANPATH "${manpath}"
>    setenv LD_LIBRARY_PATH "${lld}"
>    -setenv ESELECT_MPI_IMP="${1}"
>    +setenv ESELECT_MPI_IMP "${1}"
>     EOF
>      
>           echo "Remember to source ${user_ev_sh} or ${user_ev_csh}"
> ================================================

Fixed in eselect-0.0.3-r1.  Also found another mistake when setting PATH for
c shells and fixed that as well.

> 
> Also, in the README file, the for loop in step 6 is incorrect:
> 
> for i in $(ls ${HOME}/.env.d/*); do
>     source ${HOME}/.env.d/${i}
> done
> 
> Results in:
> 
> -bash: /home/bgreen/.env.d//home/bgreen/.env.d/mpi.csh: No such file or directory
> -bash: /home/bgreen/.env.d//home/bgreen/.env.d/mpi.sh: No such file or directoryA

Also fixed.  You might also want to check out the doc I've been working on
lately, http://dev.gentoo.org/~jsbronder/empi.xml.  Hopefully it's a little
more up to date.

> 
> 
> On the system where I'm using empi, I've created files in /etc/profile.d to
> source the user's .env.d files when they log in.  What do you think about
> having the eselect-mpi ebuild install these, so mpi users dont have to do
> that part manually?  They would instead just have to source /etc/profile or
> /etc/csh.login after running 'eselect mpi'.

Love it, I had not even thought of using this mechanism before even though I
should have.  It will also simplify switching from an mpi environment to one
without it.  I'll try to get something checked into the overlay soon,
shouldn't be more than a few days.

> 
> 
> Here are my versions of the files in /etc/profile.d:
> 
> ==============
> mpi-config.sh
> ==============
> if [ -d ${HOME}/.env.d ]; then
>     for i in ${HOME}/.env.d/*.sh ; do
>         . "${i}"
>     done
>     unset i
> fi
> 
> ==============
> mpi-config.csh
> ==============
> if ( -d ${HOME}/.env.d ) then
>     set nonomatch
>     foreach i ( ${HOME}/.env.d/*.csh )
>         source ${i}
>     end
>     unset i nonomatch
> endif
> 
> ==============
> 
> -bryan

Thanks again for testing and your comments, they're much appreciated.

-- 
Justin Bronder

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[gentoo-cluster] Re: eselect-mpi issues

[Justin Bronder]

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On 12/06/08 23:02 -0400, Justin Bronder wrote:
> > On the system where I'm using empi, I've created files in /etc/profile.d to
> > source the user's .env.d files when they log in.  What do you think about
> > having the eselect-mpi ebuild install these, so mpi users dont have to do
> > that part manually?  They would instead just have to source /etc/profile or
> > /etc/csh.login after running 'eselect mpi'.
> 
> Love it, I had not even thought of using this mechanism before even though I
> should have.  It will also simplify switching from an mpi environment to one
> without it.  I'll try to get something checked into the overlay soon,
> shouldn't be more than a few days.
> 

Added to eselect-mpi-0.0.4 which I just bumped in the overlay.

Thanks,
-- 
Justin Bronder

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Re: [gentoo-cluster] Re: eselect-mpi issues

[Eric Thibodeau]

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Justin Bronder wrote:
> On 12/06/08 11:28 -0700, Bryan Green wrote:
>   
>> Hello,
>>
>> I'm beginning to give empi/eselect-mpi a try.  Bravo, Justin, for making
>> these!
>>     
>
> Thanks for trying them out, I'm hoping someone else finds them as useful as I
> have.
>   
It is planned to be part of the Gentoo Clustering LiveCD ;)
>   
>> I've run into one bug in eselect-mpi that effects csh users (a popular
>> shell where I work).  There is simply one setenv line that has bash syntax
>> rather than csh syntax.  I already submitted a bug: its bug 226105.
>> Here is the patch to fix it:
>>
>> ================================================
>> --- files/mpi.eselect-0.0.3     (revision 1137)
>> +++ files/mpi.eselect-0.0.3     (working copy)
>> @@ -161,7 +161,7 @@
>>  setenv PATH "${binpath}"
>>   setenv MANPATH "${manpath}"
>>    setenv LD_LIBRARY_PATH "${lld}"
>>    -setenv ESELECT_MPI_IMP="${1}"
>>    +setenv ESELECT_MPI_IMP "${1}"
>>     EOF
>>      
>>           echo "Remember to source ${user_ev_sh} or ${user_ev_csh}"
>> ================================================
>>     
>
> Fixed in eselect-0.0.3-r1.  Also found another mistake when setting PATH for
> c shells and fixed that as well.
>
>   
>> Also, in the README file, the for loop in step 6 is incorrect:
>>
>> for i in $(ls ${HOME}/.env.d/*); do
>>     source ${HOME}/.env.d/${i}
>> done
>>
>> Results in:
>>
>> -bash: /home/bgreen/.env.d//home/bgreen/.env.d/mpi.csh: No such file or directory
>> -bash: /home/bgreen/.env.d//home/bgreen/.env.d/mpi.sh: No such file or directoryA
>>     
>
> Also fixed.  You might also want to check out the doc I've been working on
> lately, http://dev.gentoo.org/~jsbronder/empi.xml.  Hopefully it's a little
> more up to date.
>   
Have to remember that one ;)
>   
>> On the system where I'm using empi, I've created files in /etc/profile.d to
>> source the user's .env.d files when they log in.  What do you think about
>> having the eselect-mpi ebuild install these, so mpi users dont have to do
>> that part manually?  They would instead just have to source /etc/profile or
>> /etc/csh.login after running 'eselect mpi'.
>>     
>
> Love it, I had not even thought of using this mechanism before even though I
> should have.  It will also simplify switching from an mpi environment to one
> without it.  I'll try to get something checked into the overlay soon,
> shouldn't be more than a few days.<
>   
Keep us posted because I will definitely  want that version!
>   
>> Here are my versions of the files in /etc/profile.d:
>>
>> ==============
>> mpi-config.sh
>> ==============
>> if [ -d ${HOME}/.env.d ]; then
>>     for i in ${HOME}/.env.d/*.sh ; do
>>         . "${i}"
>>     done
>>     unset i
>> fi
>>
>> ==============
>> mpi-config.csh
>> ==============
>> if ( -d ${HOME}/.env.d ) then
>>     set nonomatch
>>     foreach i ( ${HOME}/.env.d/*.csh )
>>         source ${i}
>>     end
>>     unset i nonomatch
>> endif
>>
>> ==============
>>
>> -bryan
>>     
>
> Thanks again for testing and your comments, they're much appreciated.
>   
Yeah, thanks you both, multi-mpi-on-1-system has always plagued me too ;)

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Re: [gentoo-cluster] Re: eselect-mpi issues

[Alexey Shvetsov]

hi all!

May be it will be better if we can choose combinations mpi_imp/compiler
for example
mpi-openmpi-gcc
mpi-openmpi-intel
and so on

for now it can be done manualy specifing CC, Fc and so on env
may be it will be better if it will be done from empi?

2008/6/16 Eric Thibodeau <kyron@neuralbs.com>:
> Justin Bronder wrote:
>
> On 12/06/08 11:28 -0700, Bryan Green wrote:
>
>
> Hello,
>
> I'm beginning to give empi/eselect-mpi a try.  Bravo, Justin, for making
> these!
>
>
> Thanks for trying them out, I'm hoping someone else finds them as useful as
> I
> have.
>
>
> It is planned to be part of the Gentoo Clustering LiveCD ;)
>
>
>
> I've run into one bug in eselect-mpi that effects csh users (a popular
> shell where I work).  There is simply one setenv line that has bash syntax
> rather than csh syntax.  I already submitted a bug: its bug 226105.
> Here is the patch to fix it:
>
> ================================================
> --- files/mpi.eselect-0.0.3     (revision 1137)
> +++ files/mpi.eselect-0.0.3     (working copy)
> @@ -161,7 +161,7 @@
>  setenv PATH "${binpath}"
>   setenv MANPATH "${manpath}"
>    setenv LD_LIBRARY_PATH "${lld}"
>    -setenv ESELECT_MPI_IMP="${1}"
>    +setenv ESELECT_MPI_IMP "${1}"
>     EOF
>
>           echo "Remember to source ${user_ev_sh} or ${user_ev_csh}"
> ================================================
>
>
> Fixed in eselect-0.0.3-r1.  Also found another mistake when setting PATH for
> c shells and fixed that as well.
>
>
>
> Also, in the README file, the for loop in step 6 is incorrect:
>
> for i in $(ls ${HOME}/.env.d/*); do
>     source ${HOME}/.env.d/${i}
> done
>
> Results in:
>
> -bash: /home/bgreen/.env.d//home/bgreen/.env.d/mpi.csh: No such file or
> directory
> -bash: /home/bgreen/.env.d//home/bgreen/.env.d/mpi.sh: No such file or
> directoryA
>
>
> Also fixed.  You might also want to check out the doc I've been working on
> lately, http://dev.gentoo.org/~jsbronder/empi.xml.  Hopefully it's a little
> more up to date.
>
>
> Have to remember that one ;)
>
>
>
> On the system where I'm using empi, I've created files in /etc/profile.d to
> source the user's .env.d files when they log in.  What do you think about
> having the eselect-mpi ebuild install these, so mpi users dont have to do
> that part manually?  They would instead just have to source /etc/profile or
> /etc/csh.login after running 'eselect mpi'.
>
>
> Love it, I had not even thought of using this mechanism before even though I
> should have.  It will also simplify switching from an mpi environment to one
> without it.  I'll try to get something checked into the overlay soon,
> shouldn't be more than a few days.<
>
>
> Keep us posted because I will definitely  want that version!
>
>
>
> Here are my versions of the files in /etc/profile.d:
>
> ==============
> mpi-config.sh
> ==============
> if [ -d ${HOME}/.env.d ]; then
>     for i in ${HOME}/.env.d/*.sh ; do
>         . "${i}"
>     done
>     unset i
> fi
>
> ==============
> mpi-config.csh
> ==============
> if ( -d ${HOME}/.env.d ) then
>     set nonomatch
>     foreach i ( ${HOME}/.env.d/*.csh )
>         source ${i}
>     end
>     unset i nonomatch
> endif
>
> ==============
>
> -bryan
>
>
> Thanks again for testing and your comments, they're much appreciated.
>
>
> Yeah, thanks you both, multi-mpi-on-1-system has always plagued me too ;)
>



-- 
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Mail to
 alexxyum@gmail.com
 alexxy@gentoo.ru
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Re: [gentoo-cluster] Re: eselect-mpi issues

[Eric Thibodeau]

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Alexey Shvetsov wrote:
> hi all!
>
> May be it will be better if we can choose combinations mpi_imp/compiler
> for example
> mpi-openmpi-gcc
> mpi-openmpi-intel
> and so on
>
> for now it can be done manualy specifing CC, Fc and so on env
> may be it will be better if it will be done from empi?
>   
You might want to go read: http://bugs.gentoo.org/show_bug.cgi?id=44132

> 2008/6/16 Eric Thibodeau <kyron@neuralbs.com>:
>   
>> Justin Bronder wrote:
>>
>> On 12/06/08 11:28 -0700, Bryan Green wrote:
>>
>>
>> Hello,
>>
>> I'm beginning to give empi/eselect-mpi a try.  Bravo, Justin, for making
>> these!
>>
>>
>> Thanks for trying them out, I'm hoping someone else finds them as useful as
>> I
>> have.
>>
>>
>> It is planned to be part of the Gentoo Clustering LiveCD ;)
>>
>>
>>
>> I've run into one bug in eselect-mpi that effects csh users (a popular
>> shell where I work).  There is simply one setenv line that has bash syntax
>> rather than csh syntax.  I already submitted a bug: its bug 226105.
>> Here is the patch to fix it:
>>
>> ================================================
>> --- files/mpi.eselect-0.0.3     (revision 1137)
>> +++ files/mpi.eselect-0.0.3     (working copy)
>> @@ -161,7 +161,7 @@
>>  setenv PATH "${binpath}"
>>   setenv MANPATH "${manpath}"
>>    setenv LD_LIBRARY_PATH "${lld}"
>>    -setenv ESELECT_MPI_IMP="${1}"
>>    +setenv ESELECT_MPI_IMP "${1}"
>>     EOF
>>
>>           echo "Remember to source ${user_ev_sh} or ${user_ev_csh}"
>> ================================================
>>
>>
>> Fixed in eselect-0.0.3-r1.  Also found another mistake when setting PATH for
>> c shells and fixed that as well.
>>
>>
>>
>> Also, in the README file, the for loop in step 6 is incorrect:
>>
>> for i in $(ls ${HOME}/.env.d/*); do
>>     source ${HOME}/.env.d/${i}
>> done
>>
>> Results in:
>>
>> -bash: /home/bgreen/.env.d//home/bgreen/.env.d/mpi.csh: No such file or
>> directory
>> -bash: /home/bgreen/.env.d//home/bgreen/.env.d/mpi.sh: No such file or
>> directoryA
>>
>>
>> Also fixed.  You might also want to check out the doc I've been working on
>> lately, http://dev.gentoo.org/~jsbronder/empi.xml.  Hopefully it's a little
>> more up to date.
>>
>>
>> Have to remember that one ;)
>>
>>
>>
>> On the system where I'm using empi, I've created files in /etc/profile.d to
>> source the user's .env.d files when they log in.  What do you think about
>> having the eselect-mpi ebuild install these, so mpi users dont have to do
>> that part manually?  They would instead just have to source /etc/profile or
>> /etc/csh.login after running 'eselect mpi'.
>>
>>
>> Love it, I had not even thought of using this mechanism before even though I
>> should have.  It will also simplify switching from an mpi environment to one
>> without it.  I'll try to get something checked into the overlay soon,
>> shouldn't be more than a few days.<
>>
>>
>> Keep us posted because I will definitely  want that version!
>>
>>
>>
>> Here are my versions of the files in /etc/profile.d:
>>
>> ==============
>> mpi-config.sh
>> ==============
>> if [ -d ${HOME}/.env.d ]; then
>>     for i in ${HOME}/.env.d/*.sh ; do
>>         . "${i}"
>>     done
>>     unset i
>> fi
>>
>> ==============
>> mpi-config.csh
>> ==============
>> if ( -d ${HOME}/.env.d ) then
>>     set nonomatch
>>     foreach i ( ${HOME}/.env.d/*.csh )
>>         source ${i}
>>     end
>>     unset i nonomatch
>> endif
>>
>> ==============
>>
>> -bryan
>>
>>
>> Thanks again for testing and your comments, they're much appreciated.
>>
>>
>> Yeah, thanks you both, multi-mpi-on-1-system has always plagued me too ;)
>>
>>     
>
>
>
>   


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Re: [gentoo-cluster] Re: eselect-mpi issues

[Alexey Shvetsov]

Yes, I know about this bug =)


2008/6/27 Eric Thibodeau <kyron@neuralbs.com>:
> Alexey Shvetsov wrote:
>
> hi all!
>
> May be it will be better if we can choose combinations mpi_imp/compiler
> for example
> mpi-openmpi-gcc
> mpi-openmpi-intel
> and so on
>
> for now it can be done manualy specifing CC, Fc and so on env
> may be it will be better if it will be done from empi?
>
>
> You might want to go read: http://bugs.gentoo.org/show_bug.cgi?id=44132
>
> 2008/6/16 Eric Thibodeau <kyron@neuralbs.com>:
>
>
> Justin Bronder wrote:
>
> On 12/06/08 11:28 -0700, Bryan Green wrote:
>
>
> Hello,
>
> I'm beginning to give empi/eselect-mpi a try.  Bravo, Justin, for making
> these!
>
>
> Thanks for trying them out, I'm hoping someone else finds them as useful as
> I
> have.
>
>
> It is planned to be part of the Gentoo Clustering LiveCD ;)
>
>
>
> I've run into one bug in eselect-mpi that effects csh users (a popular
> shell where I work).  There is simply one setenv line that has bash syntax
> rather than csh syntax.  I already submitted a bug: its bug 226105.
> Here is the patch to fix it:
>
> ================================================
> --- files/mpi.eselect-0.0.3     (revision 1137)
> +++ files/mpi.eselect-0.0.3     (working copy)
> @@ -161,7 +161,7 @@
>  setenv PATH "${binpath}"
>   setenv MANPATH "${manpath}"
>    setenv LD_LIBRARY_PATH "${lld}"
>    -setenv ESELECT_MPI_IMP="${1}"
>    +setenv ESELECT_MPI_IMP "${1}"
>     EOF
>
>           echo "Remember to source ${user_ev_sh} or ${user_ev_csh}"
> ================================================
>
>
> Fixed in eselect-0.0.3-r1.  Also found another mistake when setting PATH for
> c shells and fixed that as well.
>
>
>
> Also, in the README file, the for loop in step 6 is incorrect:
>
> for i in $(ls ${HOME}/.env.d/*); do
>     source ${HOME}/.env.d/${i}
> done
>
> Results in:
>
> -bash: /home/bgreen/.env.d//home/bgreen/.env.d/mpi.csh: No such file or
> directory
> -bash: /home/bgreen/.env.d//home/bgreen/.env.d/mpi.sh: No such file or
> directoryA
>
>
> Also fixed.  You might also want to check out the doc I've been working on
> lately, http://dev.gentoo.org/~jsbronder/empi.xml.  Hopefully it's a little
> more up to date.
>
>
> Have to remember that one ;)
>
>
>
> On the system where I'm using empi, I've created files in /etc/profile.d to
> source the user's .env.d files when they log in.  What do you think about
> having the eselect-mpi ebuild install these, so mpi users dont have to do
> that part manually?  They would instead just have to source /etc/profile or
> /etc/csh.login after running 'eselect mpi'.
>
>
> Love it, I had not even thought of using this mechanism before even though I
> should have.  It will also simplify switching from an mpi environment to one
> without it.  I'll try to get something checked into the overlay soon,
> shouldn't be more than a few days.<
>
>
> Keep us posted because I will definitely  want that version!
>
>
>
> Here are my versions of the files in /etc/profile.d:
>
> ==============
> mpi-config.sh
> ==============
> if [ -d ${HOME}/.env.d ]; then
>     for i in ${HOME}/.env.d/*.sh ; do
>         . "${i}"
>     done
>     unset i
> fi
>
> ==============
> mpi-config.csh
> ==============
> if ( -d ${HOME}/.env.d ) then
>     set nonomatch
>     foreach i ( ${HOME}/.env.d/*.csh )
>         source ${i}
>     end
>     unset i nonomatch
> endif
>
> ==============
>
> -bryan
>
>
> Thanks again for testing and your comments, they're much appreciated.
>
>
> Yeah, thanks you both, multi-mpi-on-1-system has always plagued me too ;)
>
>
>
>
>



-- 
Gentoo GNU/Linux 2.6.25

Mail to
 alexxyum@gmail.com
 alexxy@gentoo.ru
-- 
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