[gmx-users] errores during compilation of GROMACS 3.3.2

Itamar Kass ikass at uq.edu.au
Mon Oct 15 12:04:48 CEST 2007 

HI Erik,

I tried this without any success. Thanks for the time.

Itamar


-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Erik Lindahl
Sent: Mon 10/15/2007 19:08
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] errores during compilation of GROMACS 3.3.2
 
Hi,

Could you try without optimization flags? Go to src/gmxlib/nonbonded/ 
nb_kernel_ia64_double and type

make nb_kernel010_ia64_double.lo CFLAGS="-O0"

It would also be useful to try running just (1) icc and (2) ias on  
the corresponding .S file.


This is probably something non-trivial that has changed in the intel  
compiler or assembler lately...


Cheers,

Erik

On Oct 15, 2007, at 10:34 AM, Itamar Kass wrote:

>
> Dear Erik,
>
> I had compiled the 3.3.1 on the same machine. The sys admin of this  
> machine is been able to compile 3.3.2 using the gnu compiler but  
> has problems with the intel one as well.
>
> Best,
> Itamar
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org on behalf of Erik Lindahl
> Sent: Mon 10/15/2007 17:02
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] errores during compilation of GROMACS 3.3.2
>
> Hi Itamar,
>
> Not immediately. Did this work fine with 3.3.1? As far as I know we
> haven't changed anything in the ia64 assembly routines.
>
> Cheers,
>
> Erik
>
> On Oct 15, 2007, at 2:16 AM, Itamar Kass wrote:
>
>> Dear all,
>>
>> I am trying to compile GROMOCS 3.3.2 on Altix 3700 BX2 (Itanium2
>> 1.6GHz). I am doing something like:
>>
>>> ./configure --prefix=/home/564/ixk564/software/gromacs --enable-
>> shared --program-suffix=_3.3.2_double --disable-float --with- 
>> fft=fftw2
>>> make -j 2
>>
>> and get in replay:
>>
>>  icc -DHAVE_CONFIG_H -I. -I../../../../src -I../../../../include -
>> DGMXLIBDIR=\"/home/564/ixk56sr4/software/gromacs/share/top\" -I/opt/
>> fftw-2.1.5/intel-8.1/include -O3 -tpp2 -ip -ftz -MT
>> nb_kernel010_ia64_double.lo -MD -MP -MF .deps/
>> nb_kernel010_ia64_double.Tpo -c nb_kernel010_ia64_double.S -o
>> nb_kernel010_ia64_double.o
>> <command line>:3:1: warning: "__PTRDIFF_TYPE__" redefined
>> <built-in>:4:1: warning: this is the location of the previous
>> definition
>> <command line>:4:1: warning: "__SIZE_TYPE__" redefined
>> <built-in>:3:1: warning: this is the location of the previous
>> definition
>> <command line>:3:1: warning: "__PTRDIFF_TYPE__" redefined
>> <built-in>:4:1: warning: this is the location of the previous
>> definition
>> <command line>:4:1: warning: "__SIZE_TYPE__" redefined
>> <built-in>:3:1: warning: this is the location of the previous
>> definition
>> /tmp/iccK7NleRs(/tmp/iccr4uV6Zs(1) : error A2040: Unexpected token:
>> Unary Diez Operator at: Start
>> /tmp/iccr4uV6Zs(2) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccr4uV6Zs(3) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccr4uV6Zs(4) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccr4uV6Zs(5) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccr4uV6Zs(6) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccr4uV6Zs(7) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccr4uV6Zs(8) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccr4uV6Zs(10) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccr4uV6Zs(15) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccr4uV6Zs(211) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccr4uV6Zs(265) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccr4uV6Zs(280) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccr4uV6Zs(520) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccr4uV6Zs(602) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> nb_kernel030_ia64_double.o - 15 error(s), 0 warning(s)
>> 1) : error A2040: Unexpected token: Unary Diez Operator at: Start
>> /tmp/iccK7NleRs(2) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccK7NleRs(3) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccK7NleRs(4) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccK7NleRs(5) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccK7NleRs(6) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccK7NleRs(7) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccK7NleRs(8) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccK7NleRs(10) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccK7NleRs(15) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccK7NleRs(194) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccK7NleRs(196) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccK7NleRs(270) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccK7NleRs(433) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> /tmp/iccK7NleRs(516) : error A2040: Unexpected token: Unary Diez
>> Operator at: Start
>> nb_kernel010_ia64_double.o - 15 error(s), 0 warning(s)
>> make[5]: *** [nb_kernel030_ia64_double.lo] Error 1
>> make[5]: *** Waiting for unfinished jobs....
>> make[5]: *** [nb_kernel010_ia64_double.lo] Error 1
>> make[5]: Leaving directory `/home/564/ixk564/software/gromacs-3.3.2/
>> src/gmxlib/nonbonded/nb_kernel_ia64_double'
>> make[4]: *** [all-recursive] Error 1
>> make[4]: Leaving directory `/home/564/ixk564/software/gromacs-3.3.2/
>> src/gmxlib/nonbonded'
>> make[3]: *** [all-recursive] Error 1
>> make[3]: Leaving directory `/home/564/ixk564/software/gromacs-3.3.2/
>> src/gmxlib'
>> make[2]: *** [all-recursive] Error 1
>> make[2]: Leaving directory `/home/564/ixk564/software/gromacs-3.3.2/
>> src'
>> make[1]: *** [all] Error 2
>> make[1]: Leaving directory `/home/564/ixk564/software/gromacs-3.3.2/
>> src'
>> make: *** [all-recursive] Error 1
>>
>> Do you have any idea how to overcome it?
>>
>> Best wishes,
>> Itamar.
>>
>> -- 
>> "Prediction is very difficult, especially about the future" - Niels
>> Bohr
>>
>> ===========================================
>> | Itamar Kass, Ph.D.
>> | Postdoctoral Research Fellow
>> |
>> | Molecular Dynamics Group
>> | School of Molecular and Microbial Sciences (SMMS)
>> | Chemistry Building (#68)
>> | The University of Queensland
>> | St. Lucia Campus, Brisbane, QLD 4067
>> | Australia
>> |
>> | Tel: +61 7 3365 9922
>> | Fax: +61 7 3365 3872
>> | E-mail: ikass at uq.edu.au
>> | Web page: http://compbio.chemistry.uq.edu.au/md/ikass/
>> ============================================
>>
>> Unless stated otherwise, this e-mail represents only the views of
>> the Sender and not the views of The University of Queensland
>>
>>
>> -- 
>> "Prediction is very difficult, especially about the future" - Niels
>> Bohr
>>
>> ===========================================
>> | Itamar Kass, Ph.D.
>> | Postdoctoral Research Fellow
>> |
>> | Molecular Dynamics Group
>> | School of Molecular and Microbial Sciences (SMMS)
>> | Chemistry Building (#68)
>> | The University of Queensland
>> | St. Lucia Campus, Brisbane, QLD 4067
>> | Australia
>> |
>> | Tel: +61 7 3365 9922
>> | Fax: +61 7 3365 3872
>> | E-mail: ikass at uq.edu.au
>> | Web page: http://compbio.chemistry.uq.edu.au/md/ikass/
>> ============================================
>>
>> Unless stated otherwise, this e-mail represents only the views of
>> the Sender and not the views of The University of Queensland
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