Fwd: Failure with compilation namd2.9-cuda_plumed1.3_recon

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Jun 24 2013 - 04:48:24 CDT

Hello:
I have managed to upload the two make.log to our server

the url are:

http://www.accademialucchese.it/images/temp/make_withrecon.log.txt
http://www.accademialucchese.it/images/temp/make_withoutrecon.log.txt

(a link is create when you select the line)

thanks
francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sat, Jun 22, 2013 at 7:15 PM
Subject: namd-l: Failure with compilation namd2.9-cuda_plumed1.3_recon
To: NAMD <namd-l_at_ks.uiuc.edu>

Hello:
Yesterday, along a thread on the status of metadynamics with namd2.9, I
alluded to my failure in compiling namd2.9-cuda4.0-plumed1.
3 with reconnaissance (Linux-86_64-g++ GTX_680). In contrast, without
calling for reconnaissance, namd executable runs well on GTX-680.

The error message on launching namd-plumed-RECON (fixing a distance in a
metalloprotein) was:
Info: Based on Charm++/Converse 60400 for multicore-linux64
Info: Built Thu Mar 21 15:42:11 CET 2013 by francesco on gig64
Info: 1 NAMD 2.9 Linux-x86_64-multicore-CUDA 6 gig64 francesco
Info: Running on 6 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.010052 s
FATAL ERROR: CUDA error on Pe 1 (gig64 device 0): All CUDA devices are in
prohibited mode, of compute capability 1.0, or otherwise unusable.
------------- Processor 1 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: CUDA error on Pe 1 (gig64 device 0): All CUDA devices
are in prohibited mode, of compute capability 1.0, or otherwise unusable.

FATAL ERROR: CUDA error on Pe 5 (gig64 device 0): All CUDA devices are in
prohibited mode, of compute capability 1.0, or otherwise unusable.
Program finished.
FATAL ERROR: CUDA error on Pe 2 (gig64 device 0): All CUDA devices are in
prohibited mode, of compute capability 1.0, or otherwise unusable.

 Both compilations were carried out with the computer equipped with two
GTX-680 cards, and the test without RECON was also carried out with two
GTX-680. In contrast, the test with RECON was run with only one GTX-680
(the other one is being replaced under guarantee). However, the compilation
without RECON works well also with a single GTX-680 in the same test.
I am not yet organized to drop the large make.log on our server. I can only
say that there is no error message and the warning messages are the same in
the two compilations. I can only add here comparative LAST SECTION the
make.log, hopefully useful.

WITH RECON:
gcc -m64 -O3 -Isb/src -Iplugins/include -DSTATIC_PLUGIN -DPSFGEN_USEPLUGINS
-I.rootdir/tcl-threaded/include -DNAMD_TCL -fexpensive-optimizations
-ffast-math -DNAMD_VERSION=\"2.9\"
-DNAMD_PLATFORM=\"Linux-x86_64-multicore-CUDA\" -DNAMD -DRECONMETAD
-DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE
-DUSE_NODEPATCHMGR -o sortreplicas obj/sortreplicas.o obj/dcdplugin.o
obj/jsplugin.o obj/namdbinplugin.o obj/pdbplugin.o obj/psfplugin.o -lm
cp .rootdir/charm-6.4.0/multicore-linux64/bin/charmrun charmrun
gcc -m64 -O3 -Isrc -I.rootdir/tcl-threaded/include -DNAMD_TCL
-fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.9\"
-DNAMD_PLATFORM=\"Linux-x86_64-multicore-CUDA\" -DNAMD -DRECONMETAD
-DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE
-DUSE_NODEPATCHMGR -o flipdcd src/flipdcd.c || \
    echo "#!/bin/sh\necho unavailable on this platform" > flipdcd; \
    chmod +x flipdcd
src/flipdcd.c: In function ‘main’:
src/flipdcd.c:42:3: warning: incompatible implicit declaration of built-in
function ‘exit’ [enabled by default]
gcc -m64 -O3 -Isrc -I.rootdir/tcl-threaded/include -DNAMD_TCL
-fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.9\"
-DNAMD_PLATFORM=\"Linux-x86_64-multicore-CUDA\" -DNAMD -DRECONMETAD
-DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE
-DUSE_NODEPATCHMGR -o flipbinpdb src/flipbinpdb.c || \
    echo "#!/bin/sh\necho unavailable on this platform" > flipbinpdb; \
    chmod +x flipbinpdb
src/flipbinpdb.c: In function ‘main’:
src/flipbinpdb.c:30:3: warning: incompatible implicit declaration of
built-in function ‘exit’ [enabled by default]
src/flipbinpdb.c:35:3: warning: incompatible implicit declaration of
built-in function ‘exit’ [enabled by default]
src/flipbinpdb.c:40:3: warning: incompatible implicit declaration of
built-in function ‘exit’ [enabled by default]
src/flipbinpdb.c:47:3: warning: incompatible implicit declaration of
built-in function ‘exit’ [enabled by default]
src/flipbinpdb.c:53:3: warning: incompatible implicit declaration of
built-in function ‘exit’ [enabled by default]
src/flipbinpdb.c:64:1: warning: incompatible implicit declaration of
built-in function ‘exit’ [enabled by default]

WITHOUT RECON:
gcc -m64 -O3 -Isb/src -Iplugins/include -DSTATIC_PLUGIN -DPSFGEN_USEPLUGINS
-I.rootdir/tcl-threaded/include -DNAMD_TCL -fexpensive-optimizations
-ffast-math -DNAMD_VERSION=\"2.9\"
-DNAMD_PLATFORM=\"Linux-x86_64-multicore-CUDA\" -DNAMD
-DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE
-DUSE_NODEPATCHMGR -o sortreplicas obj/sortreplicas.o obj/dcdplugin.o
obj/jsplugin.o obj/namdbinplugin.o obj/pdbplugin.o obj/psfplugin.o -lm
cp .rootdir/charm-6.4.0/multicore-linux64/bin/charmrun charmrun
gcc -m64 -O3 -Isrc -I.rootdir/tcl-threaded/include -DNAMD_TCL
-fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.9\"
-DNAMD_PLATFORM=\"Linux-x86_64-multicore-CUDA\" -DNAMD
-DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE
-DUSE_NODEPATCHMGR -o flipdcd src/flipdcd.c || \
    echo "#!/bin/sh\necho unavailable on this platform" > flipdcd; \
    chmod +x flipdcd
src/flipdcd.c: In function ‘main’:
src/flipdcd.c:42:3: warning: incompatible implicit declaration of built-in
function ‘exit’ [enabled by default]
gcc -m64 -O3 -Isrc -I.rootdir/tcl-threaded/include -DNAMD_TCL
-fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.9\"
-DNAMD_PLATFORM=\"Linux-x86_64-multicore-CUDA\" -DNAMD
-DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE
-DUSE_NODEPATCHMGR -o flipbinpdb src/flipbinpdb.c || \
    echo "#!/bin/sh\necho unavailable on this platform" > flipbinpdb; \
    chmod +x flipbinpdb
src/flipbinpdb.c: In function ‘main’:
src/flipbinpdb.c:30:3: warning: incompatible implicit declaration of
built-in function ‘exit’ [enabled by default]
src/flipbinpdb.c:35:3: warning: incompatible implicit declaration of
built-in function ‘exit’ [enabled by default]
src/flipbinpdb.c:40:3: warning: incompatible implicit declaration of
built-in function ‘exit’ [enabled by default]
src/flipbinpdb.c:47:3: warning: incompatible implicit declaration of
built-in function ‘exit’ [enabled by default]
src/flipbinpdb.c:53:3: warning: incompatible implicit declaration of
built-in function ‘exit’ [enabled by default]
src/flipbinpdb.c:64:1: warning: incompatible implicit declaration of
built-in function ‘exit’ [enabled by default]

Thanks a lot for your kind attention
francesco pietra

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