[gmx-users] Re: installation problem on Compaq Alpha ev68 with Tru64 unix OS (Erik Lindahl)
Wei Fu
fuwei at adrik.bchs.uh.edu
Mon Dec 15 22:55:01 CET 2003
Hi, Erik,
Thanks for your reply.
I have solved the "dos2unix" problem, but the new problem were found as follows when I execute make command.
*******************************************************************************************
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cc: Info: index.c, line 259: In the initializer for chains[1], "pnoh" does not h
ave a constant address, but occurs in a context that requires an address constan
t. This is an extension of the language. (addrconstext)
const char **chains[] = { NULL,pnoh,calpha,bb,mc,mcb,mch,mch,mch,pnodum };
---------------------------------^
cc: Info: index.c, line 259: In the initializer for chains[2], "calpha" does not
have a constant address, but occurs in a context that requires an address const
ant. This is an extension of the language. (addrconstext)
const char **chains[] = { NULL,pnoh,calpha,bb,mc,mcb,mch,mch,mch,pnodum };
--------------------------------------^
cc: Info: index.c, line 259: In the initializer for chains[3], "bb" does not hav
e a constant address, but occurs in a context that requires an address constant.
This is an extension of the language. (addrconstext)
const char **chains[] = { NULL,pnoh,calpha,bb,mc,mcb,mch,mch,mch,pnodum };
---------------------------------------------^
cc: Info: index.c, line 259: In the initializer for chains[4], "mc" does not hav
e a constant address, but occurs in a context that requires an address constant.
This is an extension of the language. (addrconstext)
const char **chains[] = { NULL,pnoh,calpha,bb,mc,mcb,mch,mch,mch,pnodum };
------------------------------------------------^
cc: Info: index.c, line 259: In the initializer for chains[5], "mcb" does not ha
ve a constant address, but occurs in a context that requires an address constant
This is an extension of the language. (addrconstext)
const char **chains[] = { NULL,pnoh,calpha,bb,mc,mcb,mch,mch,mch,pnodum };
---------------------------------------------------^
cc: Info: index.c, line 259: In the initializer for chains[6], "mch" does not ha
ve a constant address, but occurs in a context that requires an address constant
This is an extension of the language. (addrconstext)
const char **chains[] = { NULL,pnoh,calpha,bb,mc,mcb,mch,mch,mch,pnodum };
-------------------------------------------------------^
@
@
const char **chains[] = { NULL,pnoh,calpha,bb,mc,mcb,mch,mch,mch,pnodum };
-------------------------------------------------------^
cc: Info: index.c, line 259: In the initializer for chains[7], "mch" does not ha
ve a constant address, but occurs in a context that requires an address constant
This is an extension of the language. (addrconstext)
const char **chains[] = { NULL,pnoh,calpha,bb,mc,mcb,mch,mch,mch,pnodum };
-----------------------------------------------------------^
cc: Info: index.c, line 259: In the initializer for chains[8], "mch" does not ha
ve a constant address, but occurs in a context that requires an address constant
This is an extension of the language. (addrconstext)
const char **chains[] = { NULL,pnoh,calpha,bb,mc,mcb,mch,mch,mch,pnodum };
---------------------------------------------------------------^
cc: Info: index.c, line 259: In the initializer for chains[9], "pnodum" does not
have a constant address, but occurs in a context that requires an address const
ant. This is an extension of the language. (addrconstext)
const char **chains[] = { NULL,pnoh,calpha,bb,mc,mcb,mch,mch,mch,pnodum };
-------------------------------------------------------------------^
>>> This is the GROMACS code generator for MD & MC inner loops
>>> It will generate single precision Fortran 77 code in file innerf.f
>>> Using gromacs invsqrt code
>>> Inlining gromacs invsqrt code
>>> Using normal solvent optimized loops
>>> Prefetching forces in loops: none
>>> Nonthreaded inner loops
>>> Vectorizing invsqrt in loops:none
>>> Generated 51216 lines of code in 156 functions
(innerf.f may take a while to compile)
cc: Warning: widget.c, line 265: In this statement, the referenced type of the p
ointer value "ptr" is const, but the referenced type of the target of this assig
nment is not. (notconstqual)
return XmStringCreate(ptr,XmSTRING_DEFAULT_CHARSET);
------------------------^
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No suffix list.
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*******************************************************************************************
And after "make install", some commands do not work.
For example:
g_dipoles: bad substitution
mdrun:
GenCap: i 0 ctx 60-60-60 Entries 1 Nodes 0-0 Railmask 1
Segmentation fault (core dumped)
I am looking forward to your reply. Thanks so much!
Best regards.
Fu Wei
2003-12-15
************************************************************
Wei Fu (Linda)
Postdoctoral Research Associate
Department of Biology and Biochemistry
University of Houston
4800 Calhoun Rd. HSC #402C
Houston, TX 77204-5001 USA
Phone:713-743-8355(o) 713-795-9270(h)
Fax:713-743-8351
Email: fuwei at adrik.bchs.uh.edu
http://adrik.bchs.uh.edu/~fuwei/
http://uh.edu
**************************************************************
>
>Message: 7
>From: Erik Lindahl <lindahl at csb.stanford.edu>
>Subject: Re: [gmx-users] installation problem on Compaq Alpha ev68 with Tru64 unix OS
>Date: Sun, 14 Dec 2003 17:41:01 -0800
>To: gmx-users at gromacs.org
>Reply-To: gmx-users at gromacs.org
>
>Hi Wei,
>
>This might be a problem with the formatting in the file - there seems
>to be dos-style carriage-return/line feed. We'll try to check it, but
>you could help us by running that file through "dos2unix" or a similar
>program, and see if that works.
>
>I *suspect* there is something else that causes your real problem, but
>those errors should be more visible once this is fixed.
>
>Cheers,
>
>Erik
>
>running
>On Dec 14, 2003, at 10:48 AM, Wei Fu wrote:
>
>> Hello,
>>
>> I install both gromacs3.1.4 and gromacs3.2.0 on Compaq
>> supercomputer (Alphaserver ev68 with Tru64 unix OS), I set MPI and
>> fftw as following:
>>
>> ____________________________________________________________
>> setenv CPPFLAGS -I/usr/local/packages/fftw-2.1.3/include
>> setenv LDFLAGS -L/usr/local/packages/fftw-2.1.3/lib
>>
>> setenv MPICC /usr/bin/cc
>> setenv LIBS "-lmpi"
>> _______________________________________________________________________
>> _________________
>> Then, execute ./configure --enable-mpi --prefix /path_name
>> --program-suffix=_mpi
>>
>> it told me: GROMACS is ready to compile.
>> _______________________________________________________________________
>> _________________
>>
>> then,
>>
>> _______________________________________________________________________
>> _________________
>> make
>>
>> the screen has some compile problem, like
>>
>> cc: Info: protonate.c, line 166: A carriage-return character was
>> encountered; it
>> is being treated as white space. (foundcr)
>>
>> --^
>> cc: Info: protonate.c, line 167: A carriage-return character was
>> encountered; it
>> is being treated as white space. (foundcr)
>> thanx(stderr);
>> ----------------^
>> cc: Info: protonate.c, line 168: A carriage-return character was
>> encountered; it
>> is being treated as white space. (foundcr)
>>
>> ^
>> cc: Info: protonate.c, line 169: A carriage-return character was
>> encountered; it
>> is being treated as white space. (foundcr)
>> return 0;
>> -----------^
>> No suffix list.
>> No suffix list.
>> No suffix list.
>> No suffix list.
>> No suffix list.
>> No suffix list.
>> No suffix list.
>> No suffix list.
>> No suffix list.
>> No suffix list.
>> No suffix list.
>> No suffix list.
>> No suffix list.
>> No suffix list.
>>
>> _______________________________________________________________________
>> _________________
>>
>> I still execute make install
>>
>> the information appears:
>>
>> Making all in html
>> No suffix list.
>> Making all in .
>> No suffix list.
>> Making all in images
>> No suffix list.
>> Making all in online
>> No suffix list.
>> No suffix list.
>> Making all in include
>> No suffix list.
>> Making all in .
>> No suffix list.
>> Making all in types
>> No suffix list.
>> Making all in man
>> No suffix list.
>> Making all in man1
>> No suffix list.
>> No suffix list.
>> No suffix list.
>>
>> The file 'core.mdrun.iam763.0' was generated in the directory:
>> /usr/users/5/fuw/gromacs-3.2.0_beta1/alphaev68-dec-osf5.1/bin
>>
>> When I run mdrun, the error information is as follows
>>
>> GenCap: i 0 ctx 60-60-60 Entries 1 Nodes 0-0 Railmask 1
>> Segmentation fault (core dumped)
>>
>> Any suggestion shall be highly appreciated !!!
>>
>>
>> Cheers,
>>
>> Linda
>>
>> 2003-12-14
>> ************************************************************
>> Wei Fu (Linda)
>> Postdoctoral Research Associate
>> Department of Biology and Biochemistry
>> University of Houston
>> 4800 Calhoun Rd. HSC #402C
>> Houston, TX 77204-5001 USA
>> Phone:713-743-8355(o) 713-795-9270(h)
>> Fax:713-743-8351
>> Email: fuwei at adrik.bchs.uh.edu
>> http://adrik.bchs.uh.edu/~fuwei/
>> **************************************************************
>>
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