From: John Saeger (list_at_whimsey.com)
Date: Thu Dec 30 2004 - 13:20:16 CST
Gosh, I'm surprise you're having a problem. (just kidding) To tell you
the truth, I've never been able to compile NAMD either. This wouldn't
bother me so much if NAMD binaries were kept up to date. There have
been no new binaries released since September 2003. So we don't have
Clustermatic 4 and we don't have Clustermatic 5. We don't have Opterons
either. But if we have a warehouse full of Dec Alphas or something like
that we're in fine shape.
I know this wasn't very helpful, but I just wanted to let you know that
you are not alone, and if you figure it out, you should tell us how you
got NAMD to compile.
John
Ruxandra Dima wrote:
> Hello,
>
> I have problems using the Namd-2.5 precompiled binaries on a Fedora Core 3
> workstation. My runs terminate randomly with the error
>
> Stack Traceback:
> [0] _ZN16ComputePatchPair6doWorkEv+0xa4 [0x8192b34]
> [1] _ZN11WorkDistrib12enqueueWorkBEP12LocalWorkMsg+0x19 [0x824b9cd]
> [2]
> _ZN19CkIndex_WorkDistrib31_call_enqueueWorkB_LocalWorkMsgEPvP11WorkDistrib+0x11
> [0x824b9ad]
> [3] CkDeliverMessageFree+0x21 [0x827c1f9]
> [4] _Z15_processHandlerPvP11CkCoreState+0x393 [0x827d5e3]
> [5] CmiHandleMessage+0x1d [0x82b5e25]
> [6] _ZN9ScriptTcl7suspendEv+0xc [0x8228c68]
> [7] _ZN9ScriptTcl13runControllerEi+0x3f [0x8228c4f]
> [8] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0xf4 [0x82292cc]
> [9] TclInvokeStringCommand+0x6d [0x82c5145]
> [10] /home/dimar/NAMD/NAMD_2.5_Linux-i686/namd2 [0x82f946a]
> [11] Tcl_EvalEx+0x1cc [0x82f9b7c]
> [12] Tcl_EvalFile+0x157 [0x82f1ce3]
> [13] _ZN9ScriptTcl3runEPc+0x1a [0x8228b76]
> [14] main+0x1d2 [0x80ed052]
> [15] __libc_start_main+0xe3 [0x7b4e33]
> [16] sinh+0x65 [0x80eaed1]
>
> The same runs worked fine on Fedora Core 1 on the same workstation.
>
> I also tried unsuccessfully to compile Namd from source on Fedora Core 3
> (gcc-3.4.2). Charm compilation fails with the message:
>
> In file included from ccs-builtins.C:11:
> ckhashtable.h: In member function `OBJ CkHashtableT<KEY, OBJ>::get(const
> KEY&) const':
> ckhashtable.h:302: error: `len' undeclared (first use this function)
> ckhashtable.h:302: error: (Each undeclared identifier is reported only
> once for each function it appears in.)
> ckhashtable.h:304: error: there are no arguments to `entry' that depend on
> a template parameter, so a declaration of `entry' must be available
> ckhashtable.h:304: error: (if you use `-fpermissive', G++ will accept your
> code, but allowing the use of an undeclared name is deprecated)
> ckhashtable.h:306: error: `layout' undeclared (first use this function)
> ckhashtable.h:310: error: there are no arguments to `inc' that depend on a
> template parameter, so a declaration of `inc' must be available
> ckhashtable.h: In member function `OBJ& CkHashtableT<KEY,
> OBJ>::getRef(const KEY&)':
> ckhashtable.h:316: error: `len' undeclared (first use this function)
> ckhashtable.h:318: error: there are no arguments to `entry' that depend on
> a template parameter, so a declaration of `entry' must be available
> ckhashtable.h:320: error: `layout' undeclared (first use this function)
> ckhashtable.h:322: error: there are no arguments to `inc' that depend on a
> template parameter, so a declaration of `inc' must be available
> In file included from ccs-builtins.C:12:
> pup.h: In member function `CkReference<T>::operator T&()':
> pup.h:662: error: there are no arguments to `peek' that depend on a
> template parameter, so a declaration of `peek' must be available
> Fatal Error by charmc in directory
> /tmp/NAMD_2.5_Source/charm/net-linux/tmp
> Command g++ -Wno-deprecated -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -O
> -I../bin/../include -c ccs-builtins.C -o ccs-builtins.o returned error
> code 1
> charmc exiting...
> make: *** [ccs-builtins.o] Error 1
>
> I would appreciate any suggestions.
>
> Thanks,
> Ruxandra
>
>
>
>
>
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