AMBER Archive (2009)

Subject: Re: [AMBER] Error in PMEMD run

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu May 07 2009 - 19:11:25 CDT

Marek,
There has been a whole other thread running about how ifort 11, various
versions, will hang if you try to use it to compile pmemd (actual mails on
the reflector right around yours...). I have recommended using ifort
10.1.021 because I know it works fine. As far as ifort 11.*, I have no
experience, but there are reports of it hanging (this is a compiler bug -
the compiler is defective). I also have coworkers that have tried to build
gaussian 03 with ifort 11.*, and it compiles, but the executables don't pass
tests. I think German Ecklenberg (I am guessing at the name - I
unfortunately cleaned up some mail and the may amber reflector postings are
not available yet) did get some version of 11 to work (might have been
11.0.084, but we are dealing with a very dim recollection here), but I would
still prefer to just trust 10.1.021... Boy, you are getting to hit all the
speed bumps... These days I would not trust any software intel releases for
about 6 months after it is released - let other guys do the bleeding on the
bleeding edge... Ross concurs with me on this one.
Best Regards - Bob
----- Original Message -----
From: "Marek Malý" <maly_at_sci.ujep.cz>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Thursday, May 07, 2009 7:59 PM
Subject: Re: [AMBER] Error in PMEMD run

Dear Ross and Bob,

first of all thank you very much for your time and effort
which really brought good result however some problem
is still present ...

OK,

Our admin installed today ifort version 11 including corresponding cc, MKL.

Here is actual LD_LIBRARY_PATH :

LD_LIBRARY_PATH=/opt/intel/impi/3.2.0.011/lib64:/opt/intel/mkl/10.1.0.015/lib/em64t:/opt/intel/cc/11.0.074/lib/intel64:/opt/intel/fc/11.0.074/lib/intel64::/opt/intel/impi/3.2/lib64

Of course first of all I tried just to compile pmemd with this new
settings but I didn't succeeded :((

Here is my configuration statement:

./configure linux_em64t ifort intelmpi

Compilation started fine but after some time it "stopped" it means just
progress stopped but not
the compilation process it means after cca 1 hour the process is still
alive see this part
of the "top" list:

30599 mmaly 20 0 61496 16m 7012 R 50 0.1 58:51.64 fortcom

But almost whole hour it was got jammed here:

.....

runmin.f90(465): (col. 11) remark: LOOP WAS VECTORIZED.
runmin.f90(482): (col. 3) remark: LOOP WAS VECTORIZED.
runmin.f90(486): (col. 3) remark: LOOP WAS VECTORIZED.
/lib/cpp -traditional -P -I/opt/intel/impi/3.2/include -DPUBFFT -DBINTRAJ
-DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
-DFFTLOADBAL_2PROC veclib.fpp veclib.f90
ifort -c -auto -tpp7 -xP -ip -O3 veclib.f90
ifort: command line remark #10148: option '-tp' not supported
gcc -c pmemd_clib.c
/lib/cpp -traditional -P -I/opt/intel/impi/3.2/include -DPUBFFT -DBINTRAJ
-DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
-DFFTLOADBAL_2PROC gb_alltasks_setup.fpp gb_alltasks_setup.f90
ifort -c -auto -tpp7 -xP -ip -O3 gb_alltasks_setup.f90
ifort: command line remark #10148: option '-tp' not supported
/lib/cpp -traditional -P -I/opt/intel/impi/3.2/include -DPUBFFT -DBINTRAJ
-DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
-DFFTLOADBAL_2PROC pme_alltasks_setup.fpp pme_alltasks_setup.f90
ifort -c -auto -tpp7 -xP -ip -O3 pme_alltasks_setup.f90
ifort: command line remark #10148: option '-tp' not supported
/lib/cpp -traditional -P -I/opt/intel/impi/3.2/include -DPUBFFT -DBINTRAJ
-DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
-DFFTLOADBAL_2PROC pme_setup.fpp pme_setup.f90
ifort -c -auto -tpp7 -xP -ip -O3 pme_setup.f90
ifort: command line remark #10148: option '-tp' not supported
pme_setup.f90(145): (col. 17) remark: LOOP WAS VECTORIZED.
pme_setup.f90(159): (col. 22) remark: LOOP WAS VECTORIZED.
pme_setup.f90(80): (col. 8) remark: LOOP WAS VECTORIZED.
pme_setup.f90(80): (col. 8) remark: LOOP WAS VECTORIZED.
/lib/cpp -traditional -P -I/opt/intel/impi/3.2/include -DPUBFFT -DBINTRAJ
-DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
-DFFTLOADBAL_2PROC get_cmdline.fpp get_cmdline.f90
ifort -c -auto -tpp7 -xP -ip -O3 get_cmdline.f90
ifort: command line remark #10148: option '-tp' not supported
/lib/cpp -traditional -P -I/opt/intel/impi/3.2/include -DPUBFFT -DBINTRAJ
-DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
-DFFTLOADBAL_2PROC master_setup.fpp master_setup.f90
ifort -c -auto -tpp7 -xP -ip -O3 master_setup.f90
ifort: command line remark #10148: option '-tp' not supported
/lib/cpp -traditional -P -I/opt/intel/impi/3.2/include -DPUBFFT -DBINTRAJ
-DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
-DFFTLOADBAL_2PROC pmemd.fpp pmemd.f90
ifort -c -auto -tpp7 -xP -ip -O3 pmemd.f90
ifort: command line remark #10148: option '-tp' not supported
<<<<-HERE IS THE LAST LINE OF THE COMPILATION PROCESS

after this one hour I killed compilation and obtained this typical
messages:

make[1]: *** Deleting file `pmemd.o'
make[1]: *** [pmemd.o] Error 2
make: *** [install] Interrupt

I really do not understand how it is possible that compiler is using 50%
of CPU for one hour and get jammed in one line ...

I have to say that compilation with old version of ifort package was
question of some minutes.

It seems to me as an typical case of "infinity" loop ...

But nevertheless then I got the idea just use the old pmemd compilation
with the new installed libraries (cc ...) and it works :)) !!!

Another situation was with SANDER but after compleet recompilation of
Amber Tools and Amber, everything is OK ( at least now :)) ).

So I think that my problem is solved but still is here some strange
question about impossiblity to finish in real time compilation
of the PMEMD with ifort11 package. Just to be complex I have to say, that
I tried pmemd instalation with original "configure" file
but also with Bob's late night one. The result is the same. Fortunately it
is not crucial problem for me now ...

So thank you both again !!!

      Best,

         Marek

Dne Thu, 07 May 2009 01:04:10 +0200 Robert Duke <rduke_at_email.unc.edu>
napsal/-a:

> Oh, very good find Ross; I have not had the experience of mixing these,
> but I bet you are right! - Bob
> ----- Original Message ----- From: "Ross Walker" <ross_at_rosswalker.co.uk>
> To: "'AMBER Mailing List'" <amber_at_ambermd.org>
> Sent: Wednesday, May 06, 2009 5:53 PM
> Subject: RE: [AMBER] Error in PMEMD run
>
>
>> Hi Marek,
>>
>>> here is the content of the LD_LIBRARY_PATH variable:
>>>
>>> LD_LIBRARY_PATH=/opt/intel/impi/3.1/lib64:/opt/intel/mkl/10.0.011/lib/e
>>> m64t:/opt
>>> /intel/cce/9.1.043/lib:/opt/intel/fce/10.1.012/lib::/opt/intel/impi/3.1
>>> /lib64
>>
>> I suspect this is the origin of your problems... You have cce v9.1.043
>> defined and fce v10.1.012 defined. I bet these are not compatible. Note
>> there is a libsvml.so in /intel/cce/9.1.043/lib/ and this comes first in
>> your LD path so will get picked up before the Fortran one. This is
>> probably
>> leading to all sorts of problems.
>>
>> My advice would be to remove the old cce library spec from the path so
>> it
>> picks up the correct libsvml. Or upgrade your cce to match the fce
>> compiler
>> version - this should probably always be done and I am surprised Intel
>> let
>> you have mixed versions this way but alas..... <sigh>
>>
>> All the best
>> Ross
>>
>>
>> /\
>> \/
>> |\oss Walker
>>
>> | Assistant Research Professor |
>> | San Diego Supercomputer Center |
>> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
>> | http://www.rosswalker.co.uk | PGP Key available on request |
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may
>> not
>> be read every day, and should not be used for urgent or sensitive
>> issues.
>>
>>
>>
>>
>>
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