Re: [gmx-users] Compilation error
On 6/2/13 9:03 AM, vidhya sankar wrote: Dear Gromacs user Thank you for your previous reply When i Compile gromacs 4.5.6 I have Gor following error collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/gromacs-4.5.6/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/gromacs-4.5.6/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/gromacs-4.5.6/src' make: *** [all-recursive] Error 1 I configure with Following Command ./configure --enable-double --with-fft=fftpack --program-suffix=_d I Have fftw3.3.2 but i have Not used that I am using the deh=fault fftpack Using fftpack will be much slower than FFTW. How to Solve this error What went wrong? No idea. The real error message precedes the output you posted. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Compilation error
Dear Gromacs user Thank you for your previous reply When i Compile gromacs 4.5.6 I have Gor following error collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/gromacs-4.5.6/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/gromacs-4.5.6/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/gromacs-4.5.6/src' make: *** [all-recursive] Error 1 I configure with Following Command ./configure --enable-double --with-fft=fftpack --program-suffix=_d I Have fftw3.3.2 but i have Not used that I am using the deh=fault fftpack How to Solve this error What went wrong? I am using gcc 4.6.3 in Ubunt12.04 OS already I have Successfully installed gromacs 4.6 it run well Thanks in ADVANCE -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Compilation error - GROMACS 4.5.1
- Original Message - From: Shachi Katira Date: Tuesday, September 28, 2010 12:56 Subject: [gmx-users] Compilation error - GROMACS 4.5.1 To: gmx-users@gromacs.org > Hi all, > > I get the following errors when I try to compile the double precision > version of GROMACS 4.5.1 using: > > ./configure --prefix=/home/shachi/gromacs --enable-double > --with-fft=fft3 --without-x You need "--with-fft=fftw3". > Errors: > > In file included from nb_kernel400_x86_64_sse2.c:24: > ../../../../include/gmx_sse2_double.h: In function `gmx_mm_sincos_pd': > ../../../../include/gmx_sse2_double.h:457: warning: implicit > declaration of function `_mm_castsi128_pd' > ../../../../include/gmx_sse2_double.h:457: error: invalid initializer > ../../../../include/gmx_sse2_double.h:514: error: incompatible type > for argument 1 of `_mm_and_pd' > ../../../../include/gmx_sse2_double.h:515: error: incompatible type > for argument 1 of `_mm_andnot_pd' > ../../../../include/gmx_sse2_double.h:516: error: incompatible type > for argument 1 of `_mm_and_pd' > ../../../../include/gmx_sse2_double.h:517: error: incompatible type > for argument 1 of `_mm_andnot_pd' > > A similar query was posted two weeks ago > (http://lists.gromacs.org/pipermail/gmx-users/2010-September/053984.html). > I'm having the same problem in spite of using gcc 4.4.4. > > I'm using CentOS 4, gcc 4.4.4 on an AMD Opteron 285 (x86_64). The FFTW > version I'm using is 3.2.2. > > It, however, compiles fine on an Intel Xeon 5462 (IA32) machine > running MacOS 10.5, gcc 4.4.4. Check out the output of configure to see what compiler it thinks it is using. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Compilation error - GROMACS 4.5.1
Hi all, I get the following errors when I try to compile the double precision version of GROMACS 4.5.1 using: ./configure --prefix=/home/shachi/gromacs --enable-double --with-fft=fft3 --without-x Errors: In file included from nb_kernel400_x86_64_sse2.c:24: ../../../../include/gmx_sse2_double.h: In function `gmx_mm_sincos_pd': ../../../../include/gmx_sse2_double.h:457: warning: implicit declaration of function `_mm_castsi128_pd' ../../../../include/gmx_sse2_double.h:457: error: invalid initializer ../../../../include/gmx_sse2_double.h:514: error: incompatible type for argument 1 of `_mm_and_pd' ../../../../include/gmx_sse2_double.h:515: error: incompatible type for argument 1 of `_mm_andnot_pd' ../../../../include/gmx_sse2_double.h:516: error: incompatible type for argument 1 of `_mm_and_pd' ../../../../include/gmx_sse2_double.h:517: error: incompatible type for argument 1 of `_mm_andnot_pd' A similar query was posted two weeks ago (http://lists.gromacs.org/pipermail/gmx-users/2010-September/053984.html). I'm having the same problem in spite of using gcc 4.4.4. I'm using CentOS 4, gcc 4.4.4 on an AMD Opteron 285 (x86_64). The FFTW version I'm using is 3.2.2. It, however, compiles fine on an Intel Xeon 5462 (IA32) machine running MacOS 10.5, gcc 4.4.4. Thanks. -Shachi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] compilation error
yimnai forlemu wrote: Hello I am using a f90 compiler ( MIPSpro Compilers: Version 7.4.2m) No. See http://www.gromacs.org/content/view/23/33/. These errors are being produced by a C compiler. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] compilation error
Hello I am using a f90 compiler ( MIPSpro Compilers: Version 7.4.2m) --- En date de : Jeu 2.4.09, Mark Abraham a écrit : De: Mark Abraham Objet: Re: [gmx-users] compilation error À: "Discussion list for GROMACS users" Date: Jeudi 2 Avril 2009, 6h08 yimnai forlemu wrote: > Hello, > > I need some help figuring out how to compile gromacs on and sgi or linux machine. > > This is the error I get after using the make command to compile gromacs. Need some suggestions. Thanks What compiler and compiler version are you using? It looks archaic, from the error messages. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] compilation error
yimnai forlemu wrote: Hello, I need some help figuring out how to compile gromacs on and sgi or linux machine. This is the error I get after using the make command to compile gromacs. Need some suggestions. Thanks What compiler and compiler version are you using? It looks archaic, from the error messages. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] compilation error
Hello,
I need some help figuring out how to compile gromacs on and sgi or linux
machine.
This is the error I get after using the make command to compile gromacs. Need
some suggestions. Thanks
source='gmx_wham.c' object='gmx_wham.lo' libtool=yes \
DEPDIR=.deps depmode=sgi /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I.
-I../../src -I../../include
-DGMXLIBDIR=\"/usr/people/forlemu/gromacs/gromacs-4.0.4/gmx4/share/top\"
-I/usr/people/forlemu/gromacs/fftw-3.2.1/include -O3
-OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON
-LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff
1174 -D__INLINE_INTRINSICS -c -o gmx_wham.lo gmx_wham.c
cc
-DHAVE_CONFIG_H -I. -I../../src -I../../include
"-DGMXLIBDIR=\"/usr/people/forlemu/gromacs/gromacs-4.0.4/gmx4/share/top\""
-I/usr/people/forlemu/gromacs/fftw-3.2.1/include -O3
-OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON
-LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff
1174 -D__INLINE_INTRINSICS -c gmx_wham.c
-Wp,-MDupdate,.deps/gmx_wham.TPlo -o gmx_wham.o
cc-1241 cc: ERROR File = gmx_wham.c, Line = 1723
A declaration cannot appear after an executable statement in a block.
static char *en_unit[5]={NULL,"kJ","kCal","kT",NULL};
^
cc-1241 cc: ERROR File = gmx_wham.c, Line = 1724
A declaration cannot appear after an executable statement in a block.
static char *en_unit_label[24]={"","E (kJ mol\\S-1\\N)","E (kcal
mol\\S-1\\N)","E (kT)",};
^
cc-1241 cc: ERROR File = gmx_wham.c, Line = 1725
A declaration cannot appear after an executable statement in a block.
static char *en_cycl[5]={NULL,"no","yes","weighted",NULL};
^
cc-1241 cc: ERROR File = gmx_wham.c, Line = 1727
A declaration cannot appear after an executable statement in a block.
t_pargs pa[] = {
^
cc-1241 cc: ERROR File = gmx_wham.c, Line = 1780
A declaration cannot appear after an executable statement in a block.
t_filenm fnm[] = {
^
cc-1241 cc: ERROR File = gmx_wham.c, Line = 1793
A declaration cannot appear after an executable statement in a block.
int
i,j,l,nfiles,nwins,nfiles2;
^
cc-1241 cc: ERROR File = gmx_wham.c, Line = 1794
A declaration cannot appear after an executable statement in a block.
t_UmbrellaHeader header;
^
cc-1241 cc: ERROR File = gmx_wham.c, Line = 1795
A declaration cannot appear after an executable statement in a block.
t_UmbrellaWindow * window=NULL;
^
cc-1241 cc: ERROR File = gmx_wham.c, Line = 1796
A declaration cannot appear after an executable statement in a block.
double *profile,maxchange=1e20;
^
cc-1241 cc: ERROR File = gmx_wham.c, Line = 1797
A declaration cannot appear after an executable statement in a block.
bool
bMinSet,bMaxSet,bAutoSet,bExact=FALSE;
^
cc-1241 cc: ERROR File = gmx_wham.c, Line = 1798
A declaration cannot appear after an executable statement in a block.
char **fninTpr,**fninPull,**fninPdo,*fnPull;
^
cc-1241 cc: ERROR File = gmx_wham.c, Line = 1799
A declaration cannot appear after an executable statement in a block.
FILE *histout,*profout;
^
cc-1241 cc: ERROR File = gmx_wham.c, Line = 1923
A declaration cannot appear after an executable statement in a block.
char ylabel[256],title[256];
^
13 errors detected in the compilation of "gmx_wham.c".
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1
(bu21)
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Re: [gmx-users] Compilation error: eNR_NBKERNEL_NR
Tandia, Adama wrote: Hello ALL: Has anyone seen this error message before when installing GROMACS? nb_kernel_x86_64_sse2.c:98: error: `eNR_NBKERNEL_NR' undeclared here (not in a function) I used the following to compile Gromacs: ./configure --prefix=$HOME/GMX332 --enable-mpi --enable-double "F77=ifort" "CC=gcc" Need help desperately! Remove F77=ifort Thanks, Adama == Adama Tandia Modeling & Simulation Corning INC USA Tel: 607 248 1036 Fax: 607 974 3405 www.corning.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Compilation error: eNR_NBKERNEL_NR
Hello ALL: Has anyone seen this error message before when installing GROMACS? nb_kernel_x86_64_sse2.c:98: error: `eNR_NBKERNEL_NR' undeclared here (not in a function) I used the following to compile Gromacs: ./configure --prefix=$HOME/GMX332 --enable-mpi --enable-double "F77=ifort" "CC=gcc" Need help desperately! Thanks, Adama == Adama Tandia Modeling & Simulation Corning INC USA Tel: 607 248 1036 Fax: 607 974 3405 www.corning.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
