Re: compiling error of NAMD2.7b1

From: Joachim Hein (j.hein_at_ed.ac.uk)
Date: Tue Apr 21 2009 - 04:18:14 CDT

Dear Bin,

the xt3 files are to my knowledge for catamount, the old OS, very few
sites use this days. If the machine has been moved (most of them are)
to what is colloquial called "compute node linux" or "CNL" you should
start with the XT architecture files. If that is all cryptic to you,
ask you local guys, whether they are using catamount or CNL. By the
way, which XT3 are you using? Did the support team not put a Namd 2.7b1
out for you?

Hope this helps
   Joachim

BIN ZHANG wrote:
> Dear peter:
>
> Thanks for your reply. I just modified the arch file according to your
> suggestion, but the exactly same error showed up again.
>
> Now my .arch file looks like:
>
> =======================================================
> NAMD_ARCH = CRAY-XT3
> CHARMARCH = mpi-crayxt3
> CHARMOPTS =
> # need -lgmalloc because normal Catamount malloc is horribly slow
>
> CXX = CC -I/usr/include -DMEMUSAGE_USE_SBRK -DNO_SOCKET -DDUMMY_VMDSOCK
> -DNOHOSTNAME -DNO_GETPWUID -DNAMD_NO_STDOUT_FLUSH -DNAMD_NO_O_EXCL
> -DMISSING_mm_cvtsd_f64
> # added the -DMISSING_mm_cvtsd_f64 flag to avoid pgi inline problem.
> CXXOPTS = -fast
> CXXNOALIASOPTS = -Msafeptr=arg,global,local,static -Minfo=all
> -Mneginfo=loop
> #CXXNOALIASOPTS = -fast -Mnodepchk -Msafeptr=arg,global,local,static
> -Minfo=all -Mneginfo=loop
> # -fastsse with -Mnodepchk -Msafeptr=arg,global,local,static produces
> bad code
>
> CC = cc
> COPTS = -fast
>
> =======================================================
>
> Thanks,
> Bin
>
>
> On Apr 20, 2009, at 11:12 AM, Peter Freddolino wrote:
>
>> You should be able to build using PGI if you add -DMISSING_mm_cvtsd_f64
>> to your build flags. The current version of the PGI compiler doesn't
>> fully support SSE2; we've already reported this as a bug to them, and it
>> will be fixed in the next release of their compiler.
>>
>> I've never compared the speed of PGI vs. gcc, certainly not on that
>> platform. The frequent comment that gcc hurts performance is in
>> comparison to icc on x86-related architectures.
>>
>> Best,
>> Peter
>>
>> BIN ZHANG wrote:
>>> Hi, Joachim:
>>>
>>> I will definitely try this. But I heard before that gcc might affect the
>>> efficiency of NAMD significantly, did you notice this?
>>>
>>> Another thing that might worth mention is that, I can compile NAMD2.6
>>> with PGI on the same machine without any problem.
>>>
>>> Thanks,
>>> Bin
>>>
>>>
>>> On Apr 20, 2009, at 4:05 AM, Joachim Hein wrote:
>>>
>>>>> zhngbn_at_gmail.com wrote:
>>>>>> Dear all:
>>>>>>
>>>>>> I was trying to compile the NAMD2.7b1 version on a CRAY-XT3
>>>>>> supercomputer, and get the following error that I do not understand.
>>>>>>
>>>>>> PGCC-W-0277-Cannot inline function _mm_set_pd - data type mismatch
>>>>>> (/opt/pgi/7.0.7/linux86-64/7.0-7/include/CC/iostream: 882)
>>>>>> PGCC-W-0277-Cannot inline function _mm_set_pd - data type mismatch
>>>>>> (/opt/pgi/7.0.7/linux86-64/7.0-7/include/CC/iostream: 883)
>>>>>> PGCC-W-0277-Cannot inline function _mm_set_pd - data type mismatch
>>>>>> (/opt/pgi/7.0.7/linux86-64/7.0-7/include/CC/iostream: 884)
>>>>>>
>>>>>> Does this look familiar to you guys? Any idea what would be the
>>>>>> problem?
>>>>>>
>>>>>> Thanks a lot.
>>>>>> Bin
>>>> Hi Bin,
>>>>
>>>> try using the gcc compiles on a Cray XT.
>>>>
>>>> module swap PrgEnv-pgi PrgEnv-gnu
>>>>
>>>> You need to do this for all: charm++, FFTW, TCL and namd
>>>>
>>>> I have no problems building XT executables with gcc and have not
>>>> received any problem reports for the ones I build (knock on wood).
>>>>
>>>> Hope this helps.
>>>>
>>>> Best wishes
>>>> Joachim
>>>>
>>>>
>>>>
>>>> --
>>>> The University of Edinburgh is a charitable body, registered in
>>>> Scotland, with registration number SC005336.
>>>>
>
>

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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