Re: Segmentation fault for the tutorial

From: Mahmood Naderan (mahmood.nt_at_gmail.com)
Date: Wed Mar 07 2018 - 12:02:02 CST

Excuse me... I decided to use the charm tar file from the namd-2.12
source package. I ran the following commands

cd namd
cd charm-6.7.1
./build charm++ multicore-linux64 --with-production
cd multicore-linux64/tests/charm++/megatest
make pgm
./pgm +p4
cd ../../../../..
tar xzf fftw-linux-x86_64.tar.gz
mv linux-x86_64 fftw
./config Linux-x86_64-g++ --charm-arch multicore-linux64 --with-cuda
--cuda-prefix /usr/local/cuda-9.0 --with-tcl --tcl-prefix
/home/mahmood/namd-2.12/namd/tcl-threaded
cd Linux-x86_64-g++
make -j4

For the last command, the full output is

mahmood_at_orca:Linux-x86_64-g++$ make -j4
if [ ! -d inc ]; then mkdir -p inc; fi
if [ ! -d obj ]; then mkdir -p obj; fi
gcc -m64 -O3 -Isrc -I/home/mahmood/namd-2.12/namd/tcl-threaded/include
-DNAMD_TCL -fexpensive-optimizations -ffast-math
-DNAMD_VERSION=\"2.12\"
-DNAMD_PLATFORM=\"Linux-x86_64-multicore-CUDA\"
-DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE
-DUSE_NODEPATCHMGR -DBONDED_CUDA -DUSE_HOMETUPLES -o flipdcd
src/flipdcd.c || \
echo "#!/bin/sh\necho unavailable on this platform" > flipdcd; \
chmod +x flipdcd
gcc -m64 -O3 -Isrc -I/home/mahmood/namd-2.12/namd/tcl-threaded/include
-DNAMD_TCL -fexpensive-optimizations -ffast-math
-DNAMD_VERSION=\"2.12\"
-DNAMD_PLATFORM=\"Linux-x86_64-multicore-CUDA\"
-DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE
-DUSE_NODEPATCHMGR -DBONDED_CUDA -DUSE_HOMETUPLES -o flipbinpdb
src/flipbinpdb.c || \
echo "#!/bin/sh\necho unavailable on this platform" > flipbinpdb; \
chmod +x flipbinpdb
make: *** No rule to make target
'/Projects/namd2/charm-6.8.2/multicore-linux64/bin/charmrun', needed
by 'charmrun'. Stop.
make: *** Waiting for unfinished jobs....
if [ ! -f inc/.exists ]; then touch inc/.exists; fi
if [ ! -f obj/.exists ]; then touch obj/.exists; fi
src/flipdcd.c: In function ‘main’:
src/flipdcd.c:42:3: warning: implicit declaration of function ‘exit’
[-Wimplicit-function-declaration]
   exit(-1);
   ^
src/flipdcd.c:42:3: warning: incompatible implicit declaration of
built-in function ‘exit’
src/flipdcd.c:42:3: note: include ‘<stdlib.h>’ or provide a
declaration of ‘exit’
src/flipdcd.c:47:9: warning: implicit declaration of function
‘strncmp’ [-Wimplicit-function-declaration]
    if ((strncmp(argv[argcount],"-S",2) == 0) ||
(strncmp(argv[argcount],"-s",2) == 0)){
         ^
src/flipbinpdb.c: In function ‘main’:
src/flipbinpdb.c:30:3: warning: implicit declaration of function
‘exit’ [-Wimplicit-function-declaration]
   exit(-1);
   ^
src/flipbinpdb.c:30:3: warning: incompatible implicit declaration of
built-in function ‘exit’
src/flipbinpdb.c:30:3: note: include ‘<stdlib.h>’ or provide a
declaration of ‘exit’
src/flipbinpdb.c:35:3: warning: incompatible implicit declaration of
built-in function ‘exit’
   exit(-1);
   ^
src/flipbinpdb.c:35:3: note: include ‘<stdlib.h>’ or provide a
declaration of ‘exit’
src/flipbinpdb.c:40:3: warning: incompatible implicit declaration of
built-in function ‘exit’
   exit(-1);
   ^
src/flipbinpdb.c:40:3: note: include ‘<stdlib.h>’ or provide a
declaration of ‘exit’
src/flipbinpdb.c:47:3: warning: incompatible implicit declaration of
built-in function ‘exit’
   exit(-1);
   ^
src/flipbinpdb.c:47:3: note: include ‘<stdlib.h>’ or provide a
declaration of ‘exit’
src/flipbinpdb.c:53:3: warning: incompatible implicit declaration of
built-in function ‘exit’
   exit(-1);
   ^
src/flipbinpdb.c:53:3: note: include ‘<stdlib.h>’ or provide a
declaration of ‘exit’
src/flipbinpdb.c:64:1: warning: incompatible implicit declaration of
built-in function ‘exit’
 exit(0);
 ^
src/flipbinpdb.c:64:1: note: include ‘<stdlib.h>’ or provide a
declaration of ‘exit’

Please note the line which says

make: *** No rule to make target
'/Projects/namd2/charm-6.8.2/multicore-linux64/bin/charmrun', needed
by 'charmrun'. Stop.

Any idea?
Regards,
Mahmood

On Wed, Mar 7, 2018 at 9:08 PM, Mahmood Naderan <mahmood.nt_at_gmail.com> wrote:
> David,
> I cloned that. Previously I ran config with --with-charm-arch according to
> the manual. Also charm tar was there in the namd source.
>
> I don not see that now. Is it fine to drop the charm option in config?
>
> Regards,
> Mahmood
>

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