[ncl-install] NCL 5.1.0 / sed problem on IA64 cluster
Mark Van Moer
mvanmoer at ncsa.illinois.edu
Tue Jun 9 08:51:58 MDT 2009
Hi Mary,
I get the same out of memory error when I try that. I'll just go ahead and skip this part.
Thanks for all your help.
Mark
----- Original Message -----
From: "Mary Haley" <haley at ucar.edu>
To: "Mark Van Moer" <mvanmoer at ncsa.illinois.edu>
Cc: "ncl-install" <ncl-install at ucar.edu>
Sent: Tuesday, June 9, 2009 9:25:32 AM GMT -06:00 US/Canada Central
Subject: Re: [ncl-install] NCL 5.1.0 / sed problem on IA64 cluster
Mark,
I honestly have no clue about this one. When you start running out of
memory during the compilation phase, this seems like more of a
compiler problem.
Can you try doing:
cd $NCARG/ni/src/mkwrap
make clean
make all install
and see what happens?
This program is used by the WRAPIT script. The WRAPIT script enables
you to wrap Fortran code and call it from NCL.
If you don't need this capability, then you can skip this part
of the build, and it won't hurt anything.
--Mary
On Mon, 8 Jun 2009, Mark Van Moer wrote:
> Hi, escaping the plus signs worked. I'm now down to a single error:
>
> Fatal compilation error: Out of memory asking for 69632.
> compilation aborted for y.tab.c (code 1)
> make[4]: *** [y.tab.o] Error 1
> make[4]: Leaving directory `/usr/projects/vis/ncl/ncl_ncarg-5.1.0/ni/src/mkwrap'
>
> It's hard to tell what's going on through the batch monitoring system on this particular cluster, but doing a make all install in that directory does slowly eat up RAM until it crashes. I requested 12GB of RAM from the queue. Any ideas about this?
>
> Thanks,
> Mark
>
>
>
> ----- Original Message -----
> From: "David Brown" <dbrown at ucar.edu>
> To: "Mark Van Moer" <mvanmoer at ncsa.illinois.edu>
> Cc: "ncl-install" <ncl-install at ucar.edu>
> Sent: Thursday, June 4, 2009 5:11:47 PM GMT -06:00 US/Canada Central
> Subject: Re: [ncl-install] NCL 5.1.0 / sed problem on IA64 cluster
>
>
> Yeah, in this case '+' turns out not to be a good choice of delimiter
> for the sed commands.
> You could try changing '-lstdc++' to '-lstdc\+\+' (just in one of
> the Makefiles that is failing first: to see if it works).
> If that doesn't work then you will have to change the sed delimiter
> in the affected commands. I think that sed can use any character for
> the delimiter. Maybe '!' or '^' would be better.
>
> On Jun 4, 2009, at 3:11 PM, Mark Van Moer wrote:
>
>> Hi Dave,
>> I think you found it.
>>
>> $ grep CTOFLIBS Makefile
>> CTOFLIBS = -lm -lifcore -lifport -lstdc++
>> @sed -e 's+SED_CC+$(CC)+' -e 's+SED_LIBSEARCH+$
>> (LIBSEARCH)+' -e 's+SED_STDDEF+$(STD_DEFINES)+' -e 's
>> +SED_PROJDEF+$(PROJECTDEFINES)+' -e 's+SED_LDCFLAGS+$
>> (CC_LDOPTIONS)+' -e 's+SED_SYSTEM_INCLUDE+$(SYSTEM_INCLUDE)
>> +' -e 's+SED_XLIB+$(XLIB)+' -e 's+SED_PNGLIB+$(PNGLIB)+' -
>> e 's+SED_CTOFLIBS+$(CTOFLIBS)+' -e 's+SED_LIBDIR+$(LIBDIR)+' -
>> e 's+SED_INCDIR+$(INCDIR)+' -e 's+SED_NCARGDIR+$(NCARGDIR)+' -
>> e 's+SED_ROBJDIR+$(ROBJDIR)+' <ncargcc.csh >ncargcc
>>
>>
>> I had added -lstdc++ to CtoFLibraries in $NCARG/config/LINUX
>> because previously I'd been getting errors like:
>>
>> /usr/projects/compilers/intel/8.1.037/lib/libifcore.so.6: undefined
>> reference to `__cxa_end_catch'
>> /usr/projects/compilers/intel/8.1.037/lib/libifcore.so.6: undefined
>> reference to `std::terminate()'
>> /usr/projects/compilers/intel/8.1.037/lib/libifcore.so.6: undefined
>> reference to `__cxa_begin_catch
>>
>> sed must be interpreting those plus signs on stdc++ as delimiters.
>>
>> Is there a better way to fix the original errors?
>
> I don't know enough about the intel compilers to answer that. Maybe
> someone else will know.
> -dave
>
>
>> Thanks,
>> Mark
>>
>> ----- Original Message -----
>> From: "David Brown" <dbrown at ucar.edu>
>> To: "Mark Van Moer" <mvanmoer at ncsa.illinois.edu>
>> Cc: "ncl-install" <ncl-install at ucar.edu>
>> Sent: Thursday, June 4, 2009 3:56:53 PM GMT -06:00 US/Canada Central
>> Subject: Re: [ncl-install] NCL 5.1.0 / sed problem on IA64 cluster
>>
>> Hi Mark,
>>
>> If you look at the Makefile in each of the directories that give the
>> error you will see that sed is run with multiple '-e' arguments for
>> each of the commands it is trying to build.
>> I am guessing that the 'expression #x' part of the error message is
>> referring to the particular '-e' argument that results in the error.
>> Following this hypothesis the failing commands are:
>> -e 's+SED_CTOFLIBS+$(CTOFLIBS)+' # for ncargcc
>> -e 's+SED_EXTRA_LDLIBS+$(EXTRA_LDLIBS)+' # for MakeNcl
>> -e 's+SED_CTOFLIBS+$(CTOFLIBS)+' # for nhlf77
>>
>> Not all the same, but looking a little further in the ncl directory,
>> you can see if you trace back the EXTRA_LDLIBS also includes
>> CTOFLIBS. Therefore my guess is that there is something that your
>> version of sed does not like about the way your CTOFLIBS is defined.
>>
>> So can you look in any of these Makefiles and see what the definition
>> of CTOFLIBS is?
>> -dave
>>
>>
>> On Jun 4, 2009, at 2:00 PM, Mark Van Moer wrote:
>>
>>> Hello, I'm attempting to build NCL 5.1.0 on an IA64 cluster. The
>>> build has three sed errors:
>>>
>>> make[5]: Entering directory `/usr/projects/vis/ncl/ncl_ncarg-5.1.0/
>>> ncarg2d/src/binscripts'
>>> sed: -e expression #9, char 45: unknown option to `s'
>>> make[5]: *** [ncargcc] Error 1
>>>
>>> Similar errors appear 2 other times later in the build:
>>>
>>> sed: -e expression #4, char 62: unknown option to `s'
>>> make[4]: *** [MakeNcl] Error 1
>>> make[4]: Leaving directory `/usr/projects/vis/ncl/ncl_ncarg-5.1.0/
>>> ni/src/ncl'
>>>
>>> sed: -e expression #5, char 45: unknown option to `s'
>>> make[4]: *** [nhlf77] Error 1
>>> make[4]: Leaving directory `/usr/projects/vis/ncl/ncl_ncarg-5.1.0/
>>> ni/src/scripts'
>>>
>>>
>>> Is sed not liking how a makefile macro is being expanded? Anyone
>>> know what I should approach troubleshooting this? Searching seems
>>> to indicate a possible problem with delimiters. Is it possible a
>>> macro is expanding that contains the delimiter?
>>>
>>> Thanks for any help,
>>> Mark
>>>
>>> --
>>> Mark Van Moer
>>> Visualization Programmer
>>> Advanced Applications Support
>>> NCSA, University of Illinois
>>> mvanmoer at ncsa.illinois.edu
>>>
>>> _______________________________________________
>>> ncl-install mailing list
>>> List instructions, subscriber options, unsubscribe:
>>> http://mailman.ucar.edu/mailman/listinfo/ncl-install
>>
>>
>> --
>> Mark Van Moer
>> Visualization Programmer
>> Advanced Applications Support
>> NCSA, University of Illinois
>> mvanmoer at ncsa.illinois.edu
>>
>
>
> --
> Mark Van Moer
> Visualization Programmer
> Advanced Applications Support
> NCSA, University of Illinois
> mvanmoer at ncsa.illinois.edu
>
> _______________________________________________
> ncl-install mailing list
> List instructions, subscriber options, unsubscribe:
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>
--
Mark Van Moer
Visualization Programmer
Advanced Applications Support
NCSA, University of Illinois
mvanmoer at ncsa.illinois.edu
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