Re: [Condor-users] condor_compile and ifort

[Nicolas GUIOT <nicolas.guiot@xxxxxxx>]

From: Nicolas GUIOT <nicolas.guiot@xxxxxxx>
To: Philipp Kolmann <kolmann@xxxxxxxxxxxxxxxx>
Subject: Re: [Condor-users] condor_compile and ifort
Date: Tue, 27 Dec 2005 14:55:11 +0100
X-Mailer: Sylpheed-Claws 1.0.4 (GTK+ 1.2.10; i386-pc-linux-gnu)

(I'm sending this answer to everyone, with luck, maybe can someone help...)

Well, actually no : I had a few zillion errors, and I have absolutely no idea on how to correct these.
If someone can help me, would be greatly appreciated...

For info : /ibpc/io/condor is condor home, and I don't know why it's talking of "/home/condor/execute..." : it's not defined anywhere, doesn't even exist...

In fact, I'm not even sure it's possible to compile with the intel fortran compiler for condor, but I was trying, just in case of...

<---------

LINKING FOR CONDOR : /usr/bin/ld.real -Bstatic /ibpc/io/condor/lib/condor_rt0.o /usr/lib/crti.o /ibpc/matrix/opt/intel_fc_80/lib/crtxi.o -static -o simulmain.out ipo_ifortkZZWzk.o -Qy -L/ibpc/matrix/opt/intel_fc_80/lib -L/usr/lib /ibpc/matrix/opt/intel_fc_80/lib/for_main.o -lifport -lifcoremt -limf -lm -lcxa -lunwind -lpthread -lirc /ibpc/io/condor/lib/libcondorzsyscall.a /ibpc/io/condor/lib/libcondor_z.a /ibpc/io/condor/lib/libcomp_libstdc++.a -lc -lirc /ibpc/matrix/opt/intel_fc_80/lib/crtxn.o /usr/lib/crtn.o
/ibpc/io/condor/lib/libcondorzsyscall.a(switches.o)(.text+0x522c): In function `__libc_write':
/home/condor/execute/dir_5849/userdir/src/condor_syscall_lib/switches.remap-LINUX.h:74: multiple definition of `__libc_write'
/usr/lib/libpthread.a(ptw-write.o)(.text+0x0): first defined here
/usr/bin/ld.real: Warning: size of symbol `__libc_write' changed from 90 in /usr/lib/libpthread.a(ptw-write.o) to 28 in /usr/lib/libpthread.a(ptw-write.o)
/ibpc/io/condor/lib/libcondorzsyscall.a(switches.o)(.text+0x5248): In function `__libc_close':
/home/condor/execute/dir_5849/userdir/src/condor_syscall_lib/switches.remap-LINUX.h:80: multiple definition of `__libc_close'
/usr/lib/libpthread.a(ptw-close.o)(.text+0x0): first defined here
/usr/bin/ld.real: Warning: size of symbol `__libc_close' changed from 79 in /usr/lib/libpthread.a(ptw-close.o) to 22 in /usr/lib/libpthread.a(ptw-close.o)
/ibpc/io/condor/lib/libcondorzsyscall.a(switches.o)(.text+0x52f4): In function `__libc_fsync':
/home/condor/execute/dir_5849/userdir/src/condor_syscall_lib/switches.remap-LINUX.h:86: multiple definition of `__libc_fsync'
/usr/lib/libpthread.a(ptw-fsync.o)(.text+0x0): first defined here
/usr/bin/ld.real: Warning: size of symbol `__libc_fsync' changed from 79 in /usr/lib/libpthread.a(ptw-fsync.o) to 22 in /usr/lib/libpthread.a(ptw-fsync.o)
/ibpc/io/condor/lib/libcondorzsyscall.a(switches.o)(.text+0x53aa): In function `__libc_open':
/home/condor/execute/dir_5849/userdir/src/condor_syscall_lib/switches.remap-LINUX.h:91: multiple definition of `__libc_open'
/usr/lib/libpthread.a(ptw-open.o)(.text+0x0): first defined here
/usr/bin/ld.real: Warning: size of symbol `__libc_open' changed from 90 in /usr/lib/libpthread.a(ptw-open.o)to 54 in /usr/lib/libpthread.a(ptw-open.o)
/ibpc/io/condor/lib/libcondorzsyscall.a(switches.o)(.text+0x53e0): In function `__libc_read':
/home/condor/execute/dir_5849/userdir/src/condor_syscall_lib/switches.remap-LINUX.h:92: multiple definition of `__libc_read'
/usr/lib/libpthread.a(ptw-read.o)(.text+0x0): first defined here
/usr/bin/ld.real: Warning: size of symbol `__libc_read' changed from 90 in /usr/lib/libpthread.a(ptw-read.o)to 28 in /usr/lib/libpthread.a(ptw-read.o)
/ibpc/io/condor/lib/libcondorzsyscall.a(switches.o)(.text+0x53fc): In function `__libc_lseek':
/home/condor/execute/dir_5849/userdir/src/condor_syscall_lib/switches.remap-LINUX.h:96: multiple definition of `__libc_lseek'
/usr/lib/libpthread.a(ptw-lseek.o)(.text+0x0): first defined here
/usr/bin/ld.real: Warning: size of symbol `__libc_lseek' changed from 33 in /usr/lib/libpthread.a(ptw-lseek.o) to 28 in /usr/lib/libpthread.a(ptw-lseek.o)
/ibpc/io/condor/lib/libcondorzsyscall.a(switches.o)(.text+0x5aca): In function `__waitpid':
/home/condor/execute/dir_5849/userdir/src/condor_syscall_lib/switches.remap-LINUX.h:198: multiple definitionof `__waitpid'
/usr/lib/libpthread.a(ptw-waitpid.o)(.text+0x0): first defined here
/usr/bin/ld.real: Warning: size of symbol `__waitpid' changed from 90 in /usr/lib/libpthread.a(ptw-waitpid.o) to 28 in /usr/lib/libpthread.a(ptw-waitpid.o)
/ibpc/io/condor/lib/libcondorzsyscall.a(switches.special.o)(.text+0x1654): In function `system':
/home/condor/execute/dir_5849/userdir/src/condor_syscall_lib/switches.special.C:1833: multiple definition of`system'
/usr/lib/libpthread.a(pt-system.o)(.text+0x0):/home/drow/debian-glibc/glibc-2.3.2.ds1/build-tree/glibc-2.3.2/linuxthreads/pt-system.c:27: first defined here
/usr/bin/ld.real: Warning: size of symbol `system' changed from 9 in /usr/lib/libpthread.a(pt-system.o) to 38 in /usr/lib/libpthread.a(pt-system.o)
/ibpc/io/condor/lib/libcondorzsyscall.a(condor_file_agent.o)(.text+0x250): In function `CondorFileAgent::open(char const*, int, int)':
/home/condor/execute/dir_5849/userdir/src/condor_ckpt/condor_file_agent.C:99: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/ibpc/matrix/opt/intel_fc_80/lib/libifcoremt.a(for_open_proc.o)(.text+0x3c56): In function `for__compute_filename':
: warning: Using 'getpwnam' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/ibpc/matrix/opt/intel_fc_80/lib/libifcoremt.a(for_open_proc.o)(.text+0x3d39): In function `for__compute_filename':
: warning: Using 'getpwuid' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/ibpc/io/condor/lib/libcondorzsyscall.a(internet.o)(.text+0x327): In function `sin_to_hostname':
/home/condor/execute/dir_5849/userdir/src/condor_util_lib/internet.c:161: warning: Using 'gethostbyaddr' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/ibpc/io/condor/lib/libcondorzsyscall.a(internet.o)(.text+0x98): In function `string_to_sin':
/home/condor/execute/dir_5849/userdir/src/condor_util_lib/internet.c:69: warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/ibpc/io/condor/lib/libcondorzsyscall.a(sock.o)(.text+0x477): In function `Sock::getportbyserv(char*)':
/home/condor/execute/dir_5849/userdir/src/condor_io/sock.C:194: warning: Using 'getservbyname' in staticallylinked applications requires at runtime the shared libraries from the glibc version used for linking
/usr/lib/libc.a(fork.o)(.text+0x0): In function `fork':
: multiple definition of `__libc_fork'
/ibpc/io/condor/lib/libcondorzsyscall.a(switches.o)(.text+0x55dc):/home/condor/execute/dir_5849/userdir/src/condor_syscall_lib/switches.remap-LINUX.h:129: first defined here
/usr/bin/ld.real: Warning: size of symbol `__libc_fork' changed from 13 in /ibpc/io/condor/lib/libcondorzsyscall.a(switches.o) to 73 in /ibpc/io/condor/lib/libcondorzsyscall.a(switches.o)
/usr/lib/libc.a(fcntl.o)(.text+0x220): In function `fcntl':
: multiple definition of `__libc_fcntl'
/ibpc/io/condor/lib/libcondorzsyscall.a(switches.o)(.text+0x52be):/home/condor/execute/dir_5849/userdir/src/condor_syscall_lib/switches.remap-LINUX.h:85: first defined here
/usr/bin/ld.real: Warning: size of symbol `__libc_fcntl' changed from 54 in /ibpc/io/condor/lib/libcondorzsyscall.a(switches.o) to 111 in /ibpc/io/condor/lib/libcondorzsyscall.a(switches.o)
/ibpc/io/condor/lib/libcondorzsyscall.a(file_state.o)(.text+0x1a0): In function `CondorFileTable::init()':
/home/condor/execute/dir_5849/userdir/src/condor_ckpt/file_state.C:179: undefined reference to `_Unwind_Resume'
/ibpc/io/condor/lib/libcondorzsyscall.a(file_state.o)(.text+0x23d):/home/condor/execute/dir_5849/userdir/src/condor_ckpt/file_state.C:180: undefined reference to `_Unwind_Resume'
/ibpc/io/condor/lib/libcondorzsyscall.a(file_state.o)(.text+0x2da):/home/condor/execute/dir_5849/userdir/src/condor_ckpt/file_state.C:181: undefined reference to `_Unwind_Resume'
/ibpc/io/condor/lib/libcondorzsyscall.a(file_state.o)(.text+0x779): In function `CondorFileTable::make_info(char*)':
/home/condor/execute/dir_5849/userdir/src/condor_ckpt/file_state.C:292: undefined reference to `_Unwind_Resume'
/ibpc/io/condor/lib/libcondorzsyscall.a(file_state.o)(.text+0x81e):/home/condor/execute/dir_5849/userdir/src/condor_ckpt/file_state.C:296: undefined reference to `_Unwind_Resume'
/ibpc/io/condor/lib/libcondorzsyscall.a(file_state.o)(.text+0xc0f):/home/condor/execute/dir_5849/userdir/src/condor_ckpt/file_state.C:453: more undefined references to `_Unwind_Resume' follow
/ibpc/io/condor/lib/libcomp_libstdc++.a(eh_catch.o)(.text.__cxa_end_catch+0x54): In function `__cxa_end_catch':
: undefined reference to `_Unwind_DeleteException'
/ibpc/io/condor/lib/libcomp_libstdc++.a(eh_personality.o)(.text._Z21base_of_encoded_valuehP15_Unwind_Context+0x63): In function `base_of_encoded_value(unsigned char, _Unwind_Context*)':
: undefined reference to `_Unwind_GetDataRelBase'
/ibpc/io/condor/lib/libcomp_libstdc++.a(eh_personality.o)(.text._Z21base_of_encoded_valuehP15_Unwind_Context+0x79): In function `base_of_encoded_value(unsigned char, _Unwind_Context*)':
: undefined reference to `_Unwind_GetRegionStart'
/ibpc/io/condor/lib/libcomp_libstdc++.a(eh_personality.o)(.text._Z21base_of_encoded_valuehP15_Unwind_Context+0x84): In function `base_of_encoded_value(unsigned char, _Unwind_Context*)':
: undefined reference to `_Unwind_GetTextRelBase'
/ibpc/io/condor/lib/libcomp_libstdc++.a(eh_personality.o)(.text._Z17parse_lsda_headerP15_Unwind_ContextPKhP16lsda_header_info+0x26): In function `parse_lsda_header(_Unwind_Context*, unsigned char const*, lsda_header_info*)':
: undefined reference to `_Unwind_GetRegionStart'
/ibpc/io/condor/lib/libcomp_libstdc++.a(eh_personality.o)(.text.__gxx_personality_v0+0x59): In function `__gxx_personality_v0':
: undefined reference to `_Unwind_GetLanguageSpecificData'
/ibpc/io/condor/lib/libcomp_libstdc++.a(eh_personality.o)(.text.__gxx_personality_v0+0xa7): In function `__gxx_personality_v0':
: undefined reference to `_Unwind_GetIP'
/ibpc/io/condor/lib/libcomp_libstdc++.a(eh_personality.o)(.text.__gxx_personality_v0+0x25d): In function `__gxx_personality_v0':
: undefined reference to `_Unwind_SetGR'
/ibpc/io/condor/lib/libcomp_libstdc++.a(eh_personality.o)(.text.__gxx_personality_v0+0x277): In function `__gxx_personality_v0':
: undefined reference to `_Unwind_SetGR'
/ibpc/io/condor/lib/libcomp_libstdc++.a(eh_personality.o)(.text.__gxx_personality_v0+0x289): In function `__gxx_personality_v0':
: undefined reference to `_Unwind_SetIP'
/ibpc/io/condor/lib/libcomp_libstdc++.a(eh_personality.o)(.text.__cxa_call_unexpected+0x122): In function `__cxa_call_unexpected':
: undefined reference to `_Unwind_Resume'
/ibpc/io/condor/lib/libcomp_libstdc++.a(eh_throw.o)(.text.__cxa_throw+0x65): In function `__cxa_throw':
: undefined reference to `_Unwind_RaiseException'
/ibpc/io/condor/lib/libcomp_libstdc++.a(eh_throw.o)(.text.__cxa_rethrow+0x2c): In function `__cxa_rethrow':
: undefined reference to `_Unwind_RaiseException'
/ibpc/io/condor/lib/libcomp_libstdc++.a(new_op.o)(.text._Znwj+0xb7): In function `operator new(unsigned int)':
: undefined reference to `_Unwind_Resume'
/ibpc/io/condor/lib/libcomp_libstdc++.a(new_opv.o)(.text._Znaj+0x2d): In function `operator new[](unsigned int)':
: undefined reference to `_Unwind_Resume'
/ibpc/io/condor/lib/libcomp_libstdc++.a(ctype.o)(.text._ZNSt5ctypeIcE13classic_tableEv+0x1e): In function `std::ctype<char>::classic_table()':
: undefined reference to `_Unwind_Resume'
/ibpc/io/condor/lib/libcomp_libstdc++.a(ctype.o)(.text._ZNSt5ctypeIcEC2EP15__locale_structPKtbj+0x88): In function `std::ctype<char>::ctype(__locale_struct*, unsigned short const*, bool, unsigned int)':
: undefined reference to `_Unwind_Resume'
/ibpc/io/condor/lib/libcomp_libstdc++.a(ctype.o)(.text._ZNSt5ctypeIcEC1EP15__locale_structPKtbj+0x88): In function `std::ctype<char>::ctype(__locale_struct*, unsigned short const*, bool, unsigned int)':
: undefined reference to `_Unwind_Resume'
/ibpc/io/condor/lib/libcomp_libstdc++.a(ctype.o)(.text._ZNSt5ctypeIwEC2EP15__locale_structj+0x54): more undefined references to `_Unwind_Resume' follow
make: *** [main] Error 1

---------->

That's it

Bye
Nicolas


----------------
On Fri, 23 Dec 2005 19:49:14 +0100
Philipp Kolmann <kolmann@xxxxxxxxxxxxxxxx> wrote:

> bon soir,
> 
> did you get your fortran program to compile with condor_compile?
> I have problems with achieving this.
> 
> thanks
> philipp
> 
> On Fri, Dec 23, 2005 at 04:14:01PM +0100, Nicolas GUIOT wrote:
> > Sorry : finally found it : 
> > 
> > just replace /usr/bin/ld with the one furnished by condor (Who said "as stated in the doc" ?): 
> >        mv /[ld-path]/ld /[ld-path]/ld.real
> >         cp /usr/local/condor/lib/ld /[ld-path]/ld
> >         chown root /[ld-path]/ld
> >         chmod 755 /[ld-path]/ld
> > 
> > Bye 
> > Nicolas
> > ----------------
> > On Fri, 23 Dec 2005 15:58:14 +0100
> > Nicolas GUIOT <nicolas.guiot@xxxxxxx> wrote:
> > 
> > > Hi 
> > > 
> > > I'm trying to condor_compile a program written in fortran, taht we usually compile with the intel fortran compiler.
> > > 
> > > But I'm getting the following error : 
> > > $ condor_compile make
> > > Usage: condor_compile <command> [options/files .... ]
> > >   where <command> is one of the following:
> > >   gcc, g++, g77, cc, acc, c89, CC, f77, fort77, ld,
> > >   pgcc, pgf77, pgf90, or pghpf.
> > >   (on some platforms, f90 is also allowed)
> > > 
> > > I went a bit through the condor_compile script, and I think it _could_ work if I had a full install of condor : But during the install process, when asked if I wanted a "full install of condor", I answered Yes, as much as I can remember (I had followed the Mike Yoder's doc : http://docs.optena.com/display/CONDOR/A+Simple+Linux+Installation) : 
> > > 
> > > So, What did I miss ?
> > > 
> > > Or : How can I "correct" this ? Is it at least possible to compile with "ifort", the intel fortran compiler ?
> > > 
> > > Thanks for any advice... and Merry Christmas :)
> > > Nicolas

-----------------------------------------------
CNRS - UPR 9080 : Laboratoire de Biochimie Theorique
Institut de Biologie Physico-Chimique
13 rue Pierre et Marie Curie
75005 PARIS - FRANCE

Tel : +33 158 41 51 70
Fax : +33 158 41 50 26
------------------------------------------------