On May 7, 2014, at 8:32 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Wed, May 07, 2014, M. Reza Ganjalikhany wrote:
>>
>> I got the following error while I was installing parallel amber12 +
>> ambertools13 with MPICH2 3.0.4 on ubuntu 14.04 x86_64. Configuration step
>> passed successfully but the error appeared during the installation:
>>
>> Obtaining the gnu suite version:
>> gcc -v
>> The version is 4.8.2
>
> What is the result of typing "mpicc -show"?
>
> Did you have any problems with this compiler when compiling in serial mode?
>
>> mpicc -c -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
>> -DHASGZ -DHASBZ2 -DMPI cifparse.c
>> cifparse.c: In function ‘ndb_cif_print_item_value’:
>> cifparse.c:180:7: error: format not a string literal and no format
>> arguments [-Werror=format-security]
>> fprintf(fp, null_char);
>> ^
>
> OK: you compiler is setting stricter error compliance than I think anyone
> has every reported here before (-Werror=format-security), and what would
> usually be a warning has become an error:
>
>> cc1: some warnings being treated as errors
>
> Try changing line 180 in cifparse.c to the following:
>
> fputs(null_char, fp);
>
> and recompile.
>
> [To developers: is anyone else using Ubuntu 14.04 and/or gcc 4.8.2? Is this
> the default setting for this compiler setup?]
4.8.2 is indeed the default compiler suite for Ubuntu 14.04 -- Ubuntu lives at the cutting edge. I have this compiler version on my machine and it builds Amber just fine (in serial and parallel, albeit with OpenMPI). The OP's mpicc wrapper has to be setting that compiler flag, which is something I've never seen before.
We would have to know how their MPI was installed to see if this error would be common enough to issue a bugfix... (Since this is the first we've seen of it, maybe it's not common?)
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 07 2014 - 06:00:10 PDT
