From: Sabuj Pattanayek (sabuj.pattanayek_at_vanderbilt.edu)
Date: Wed Mar 15 2006 - 09:50:11 CST
Hi,
I recompiled fftw and tcl using --enable-static and --disable-shared
respectively, cleaned out the compile directory and started a new
compile, I am getting different linking errors, from glibc?:
gcc -Isb/src -I/sb/apps/tcltk-8.4.12/Linux2/i686/include -DNAMD_TCL
-DUSE_NON_CONST -O3 -march=i686 -static -DNAMD_VERSION=\"2.6b1\"
-DNAMD_PLATFORM=\"Linux-i686-MPI\" -o psfgen obj/tcl_main.o
obj/tcl_psfgen.o obj/charmm_file.o obj/charmm_parse_topo_defs.o
obj/extract_alias.o obj/hash.o obj/hasharray.o obj/memarena.o
obj/pdb_file.o obj/pdb_file_extract.o obj/psf_file.o
obj/psf_file_extract.o obj/topo_defs.o obj/topo_mol.o
obj/topo_mol_output.o obj/stringhash.o
-L/sb/apps/tcltk-8.4.12/Linux2/i686/lib -ltcl8.4 -ldl -lm
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclLoadDl.o)(.text+0x2a):
In function `TclpDlopen':
: warning: Using 'dlopen' in statically linked applications requires at
runtime the shared libraries from the glibc version used for linking
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixFCmd.o)(.text+0xd83):
In function `GetGroupAttribute':
: warning: Using 'getgrgid' in statically linked applications requires
at runtime the shared libraries from the glibc version used for linking
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixFCmd.o)(.text+0xfb1):
In function `SetGroupAttribute':
: warning: Using 'getgrnam' in statically linked applications requires
at runtime the shared libraries from the glibc version used for linking
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixFCmd.o)(.text+0xdbb):
In function `GetGroupAttribute':
: warning: Using 'endgrent' in statically linked applications requires
at runtime the shared libraries from the glibc version used for linking
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixFCmd.o)(.text+0x10c9):
In function `SetOwnerAttribute':
: warning: Using 'getpwnam' in statically linked applications requires
at runtime the shared libraries from the glibc version used for linking
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixFCmd.o)(.text+0xe4f):
In function `GetOwnerAttribute':
: warning: Using 'getpwuid' in statically linked applications requires
at runtime the shared libraries from the glibc version used for linking
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixFCmd.o)(.text+0xe8b):
In function `GetOwnerAttribute':
: warning: Using 'endpwent' in statically linked applications requires
at runtime the shared libraries from the glibc version used for linking
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixChan.o)(.text+0x171a):
In function `TcpGetOptionProc':
: warning: Using 'gethostbyaddr' in statically linked applications
requires at runtime the shared libraries from the glibc version used for
linking
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixChan.o)(.text+0x1acd):
In function `CreateSocketAddress':
: warning: Using 'gethostbyname' in statically linked applications
requires at runtime the shared libraries from the glibc version used for
linking
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclIOSock.o)(.text+0x46):
In function `TclSockGetPort':
: warning: Using 'getservbyname' in statically linked applications
requires at runtime the shared libraries from the glibc version used for
linking
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x1d):
In function `TclpThreadCreate':
: undefined reference to `pthread_attr_init'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x27):
In function `TclpThreadCreate':
: undefined reference to `pthread_attr_setscope'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x44):
In function `TclpThreadCreate':
: undefined reference to `pthread_create'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x5c):
In function `TclpThreadCreate':
: undefined reference to `pthread_attr_destroy'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x72):
In function `TclpThreadCreate':
: undefined reference to `pthread_attr_setstacksize'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x87):
In function `TclpThreadCreate':
: undefined reference to `pthread_attr_setdetachstate'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x9a):
In function `TclpThreadCreate':
: undefined reference to `pthread_create'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0xb2):
In function `TclpThreadCreate':
: undefined reference to `pthread_create'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0xc7):
In function `TclpThreadCreate':
: undefined reference to `pthread_attr_destroy'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0xf2):
In function `Tcl_JoinThread':
: undefined reference to `pthread_join'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x11f):
In function `TclpThreadExit':
: undefined reference to `pthread_exit'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x136):
In function `Tcl_GetCurrentThread':
: undefined reference to `pthread_self'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x15b):
In function `TclpInitLock':
: undefined reference to `pthread_mutex_lock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x17f):
In function `TclFinalizeLock':
: undefined reference to `pthread_mutex_unlock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x1a3):
In function `TclpInitUnlock':
: undefined reference to `pthread_mutex_unlock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x1c7):
In function `TclpMasterLock':
: undefined reference to `pthread_mutex_lock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x1eb):
In function `TclpMasterUnlock':
: undefined reference to `pthread_mutex_unlock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x22f):
In function `Tcl_MutexLock':
: undefined reference to `pthread_mutex_lock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x24a):
In function `Tcl_MutexLock':
: undefined reference to `pthread_mutex_lock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x25e):
In function `Tcl_MutexLock':
: undefined reference to `pthread_mutex_unlock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x26c):
In function `Tcl_MutexLock':
: undefined reference to `pthread_mutex_lock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x28a):
In function `Tcl_MutexLock':
: undefined reference to `pthread_mutex_init'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x2b9):
In function `Tcl_MutexUnlock':
: undefined reference to `pthread_mutex_unlock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x2e7):
In function `TclpFinalizeMutex':
: undefined reference to `pthread_mutex_destroy'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x327):
In function `TclpThreadDataKeyInit':
: undefined reference to `pthread_mutex_lock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x33b):
In function `TclpThreadDataKeyInit':
: undefined reference to `pthread_mutex_unlock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x35a):
In function `TclpThreadDataKeyInit':
: undefined reference to `pthread_key_create'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x372):
In function `TclpThreadDataKeyInit':
: undefined reference to `pthread_mutex_unlock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x3a2):
In function `TclpThreadDataKeyGet':
: undefined reference to `pthread_getspecific'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x3ce):
In function `TclpThreadDataKeySet':
: undefined reference to `pthread_setspecific'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x402):
In function `TclpFinalizeThreadData':
: undefined reference to `pthread_getspecific'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x41d):
In function `TclpFinalizeThreadData':
: undefined reference to `pthread_setspecific'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x45a):
In function `TclpFinalizeThreadDataKey':
: undefined reference to `pthread_key_delete'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x51b):
In function `Tcl_ConditionWait':
: undefined reference to `pthread_cond_timedwait'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x537):
In function `Tcl_ConditionWait':
: undefined reference to `pthread_mutex_lock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x54c):
In function `Tcl_ConditionWait':
: undefined reference to `pthread_mutex_unlock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x572):
In function `Tcl_ConditionWait':
: undefined reference to `pthread_cond_wait'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x593):
In function `Tcl_ConditionWait':
: undefined reference to `pthread_cond_init'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x5cb):
In function `Tcl_ConditionNotify':
: undefined reference to `pthread_cond_broadcast'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x5fb):
In function `TclpFinalizeCondition':
: undefined reference to `pthread_cond_destroy'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x6c4):
In function `TclpNewAllocMutex':
: undefined reference to `pthread_mutex_init'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x708):
In function `TclpFreeAllocMutex':
: undefined reference to `pthread_mutex_destroy'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x75c):
In function `TclpFreeAllocCache':
: undefined reference to `pthread_key_delete'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x795):
In function `TclpGetAllocCache':
: undefined reference to `pthread_getspecific'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x7aa):
In function `TclpGetAllocCache':
: undefined reference to `pthread_mutex_lock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x7c5):
In function `TclpGetAllocCache':
: undefined reference to `pthread_mutex_unlock'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x7d6):
In function `TclpGetAllocCache':
: undefined reference to `pthread_getspecific'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x7f0):
In function `TclpGetAllocCache':
: undefined reference to `pthread_key_create'
/sb/apps/tcltk-8.4.12/Linux2/i686/lib/libtcl8.4.a(tclUnixThrd.o)(.text+0x821):
In function `TclpSetAllocCache':
: undefined reference to `pthread_setspecific'
collect2: ld returned 1 exit status
make: *** [psfgen] Error 1
Thanks,
Sabuj Pattanayek
Brian Bennion wrote:
>
>
> You should review the compilation instructions for NAMD on the NAMDwiki
> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdCompile
>
> NAMD is statically linked to tcl and fftw ie uses libtcl8.4.a libraries
> not .so files...
>
>
>
> On Mon, 13 Mar 2006, Sabuj Pattanayek wrote:
>
>> Hi,
>>
>> I almost have namd compiled but it errored during the linking stage. I
>> have install tcltk-8.4.12 in a separate directory and I put the
>> following in the arch/Linux-i686.tcl file:
>>
>> TCLDIR=/sb/apps/tcltk-8.4.12/Linux2/i686
>> TCLINCL=-I$(TCLDIR)/include
>> TCLLIB=-L$(TCLDIR)/lib -ltcl8.4 -ldl
>> TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST
>> TCL=$(TCLINCL) $(TCLFLAGS)
>>
>> All is well during the compile stage until it tries to link everything
>> and I get this error:
>>
>> /usr/bin/ld: cannot find -ltcl8.4
>>
>> I'm not sure why this is happening because libtcl8.4.so exists in the
>> lib directory defined by TCLDIR. I also tried linking libtcl8.4.so to
>> libtcl.so and using -ltcl in the arch/Linux-i686.tcl file but I also
>> receive the same error. Does anyone know why this might be happening?
>> Does namd only link with a tcltk-8.3.x revision?
>>
>> Thanks,
>> Sabuj Pattanayek
>>
>
> ************************************************
> Brian Bennion, Ph.D.
> Biosciences Directorate
> Lawrence Livermore National Laboratory
> P.O. Box 808, L-448 bennion1_at_llnl.gov
> 7000 East Avenue phone: (925) 422-5722
> Livermore, CA 94550 fax: (925) 424-6605
> ************************************************
>
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