Hi,
Serial compilation of amber was alright but the parallel compilation is not
possible.
Here is the result for mpicc -show:
cc -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4
-Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro
-I/usr/include/mpich -L/usr/lib/x86_64-linux-gnu -lmpich -lopa -lmpl -lrt
-lcr -lpthread
and also
I changed line 180 in cifparse.c to what you suggested [ fputs(null_char,
fp); ] but again the following error appeared:
.
.
.
Command.c: In function ‘GetFitNamelist’:
Command.c:1159:10: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result [-Wunused-result]
fgets(line, MAXLINE, inp);
^
mpicc -c -O3 -mtune=native -DSYSV -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI
-I/opt/amber12/include -o Constraints.o Constraints.c
mpicc -c -O3 -mtune=native -DSYSV -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI
-I/opt/amber12/include -o Thermostats.o Thermostats.c
mpicc -c -O3 -mtune=native -DSYSV -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI
-I/opt/amber12/include -o Barostats.o Barostats.c
mpicc -c -O3 -mtune=native -DSYSV -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI
-I/opt/amber12/include -o Integrator.o Integrator.c
mpicc -c -O3 -mtune=native -DSYSV -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI
-I/opt/amber12/include -o Timings.o Timings.c
mpicc -c -O3 -mtune=native -DSYSV -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI
-I/opt/amber12/include -o Manual.o Manual.c
mpicc -c -O3 -mtune=native -DSYSV -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI
-I/opt/amber12/include -o VirtualSites.o VirtualSites.c
VirtualSites.c: In function ‘ReadEPRuleFile’:
VirtualSites.c:168:12: warning: ignoring return value of ‘fgets’, declared
with attribute warn_unused_result [-Wunused-result]
fgets(line, MAXLINE, inp);
^
mpicc -c -O3 -mtune=native -DSYSV -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI
-I/opt/amber12/include -o Buckingham.o Buckingham.c
mpicc -c -O3 -mtune=native -DSYSV -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI
-I/opt/amber12/include -o ThermoDyn.o ThermoDyn.c
mpicc -c -O3 -mtune=native -DSYSV -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI
-I/opt/amber12/include -o ChargeFit.o ChargeFit.c
ChargeFit.c: In function ‘AssignGridTopologies’:
ChargeFit.c:80:7: error: format not a string literal and no format
arguments [-Werror=format-security]
sprintf(myfit->tpname.map[i], tp->source);
^
ChargeFit.c:82:2: error: format not a string literal and no format
arguments [-Werror=format-security]
sprintf(myfit->eprule.map[i], tp->eprulesource);
^
ChargeFit.c: In function ‘ReadEPotGrid’:
ChargeFit.c:328:10: warning: ignoring return value of ‘fgets’, declared
with attribute warn_unused_result [-Wunused-result]
fgets(line, 128, inp);
^
ChargeFit.c:346:9: warning: ignoring return value of ‘fscanf’, declared
with attribute warn_unused_result [-Wunused-result]
fscanf(inp, "%d%lf%lf%lf", &i, &lvec[0], &lvec[1], &lvec[2]);
^
ChargeFit.c:347:9: warning: ignoring return value of ‘fscanf’, declared
with attribute warn_unused_result [-Wunused-result]
fscanf(inp, "%d%lf%lf%lf", &j, &lvec[3], &lvec[4], &lvec[5]);
^
ChargeFit.c:348:9: warning: ignoring return value of ‘fscanf’, declared
with attribute warn_unused_result [-Wunused-result]
fscanf(inp, "%d%lf%lf%lf", &k, &lvec[6], &lvec[7], &lvec[8]);
^
ChargeFit.c:354:11: warning: ignoring return value of ‘fscanf’, declared
with attribute warn_unused_result [-Wunused-result]
fscanf(inp, "%d%lf%lf%lf%lf", &j, &nucchg[i], &crd->loc[3*i],
^
ChargeFit.c:369:8: warning: ignoring return value of ‘fscanf’, declared
with attribute warn_unused_result [-Wunused-result]
fscanf(inp, "%f", &ftmp[k]);
^
cc1: some warnings being treated as errors
make[2]: *** [ChargeFit.o] Error 1
make[2]: Leaving directory `/opt/amber12/AmberTools/src/mdgx'
make[1]: *** [parallel] Error 2
make[1]: Leaving directory `/opt/amber12/AmberTools/src'
make: *** [install] Error 2
On Wed, May 7, 2014 at 5:02 PM, 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?]
>
> ...thanks for the report...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri May 09 2014 - 23:30:03 PDT
