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undefined reference to __ctype_b
#10496 05/09/06 11:01 AM
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freesky Offline OP
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When I installed charmm c32b2 on our linux cluster, it failed to generate the executable file. I installed charmm with below options,

./install.com gnu large FULL G77 M mpich X

Part of the output in gnu.log:

mpi/libmpich.a(p4_procgroup.o)(.text+0x1d5): In function `read_procgroup':
: undefined reference to `__ctype_b'
collect2: ld returned 1 exit status
hf77: No such file or directory
make: *** [/home/charmm/c32b2/exec/gnu/charmm] Error 1


Does anyone have suggestions on this error?
Thanks.

Sheng

Re: undefined reference to __ctype_b
freesky #10497 05/09/06 09:57 PM
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rmv Online Content
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I don't believe there is a 'G77' option for install.com; also, 'FULL' is the default and isn't really needed.

I recommend using the 'X' option only with single-threaded (non-parallel) executables.

What is hf77?

Is your PATH set up properly to use mpif77?

Can you compile and run the MPICH test programs?

Have you compiled a simple executable yet, via e.g.

install.com gnu large


Rick Venable
computational chemist

Re: undefined reference to __ctype_b
rmv #10498 05/11/06 03:01 AM
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freesky Offline OP
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hf77 is the same as mpif77.

I found on the web that this error arised from a bug of glibc-2.3.2. I recompiled the mpich-1.2.7p1 using pgi compilers and used pgf77(pgf90) to compile charmm source files, and succeeded to install charmm.


Sheng

Re: undefined reference to __ctype_b
freesky #10499 05/11/06 04:44 PM
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I would like to run c32b2 using FREE compilers on a single dual-opteron machine (fedora core 5). Is there any advice how to succeed in this attempt ? My last attempts ended up in a syntax error during compilation:(. I did not use mpi - is this absolutely essantial for running charmm c32b2?

many thanks in advance for some hints to success,
David

Re: undefined reference to __ctype_b
greenhorn #10500 05/11/06 05:41 PM
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If you use a relevant subject line you increase the chances that somebody will provide the information you seek.
MPI is free, but not necessary to run CHARMM.
intel's ifort compiler is almost free (actually free to people who fulfil the intel non-commercial criterion) and quite good.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: undefined reference to __ctype_b
lennart #10501 05/11/06 06:05 PM
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rmv Online Content
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The Intel compiler license technically restricts the "free" part to people who are not being paid for the work that they do with the compiler. As such it is free to undergraduate students, but not for post-docs and professors if they use it for work they are being paid to do.


Rick Venable
computational chemist

c32b2 compilation using intel compiler
rmv #10502 07/12/06 01:42 PM
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Hi,
...are there any experiences with c32b2 compilation with the intel compiler on a AMD opteron platform ? many thanks for some helpful information ("tutorial"?) in advance, David
P.S.: Use of gnu compiler g77/gfortran seemed to be straightforward in the beginning but [after increase of system size] it became a NIGHTMARE )

NO stable c32b2 installation for AMD Opteron possible ?!?
greenhorn #10503 07/17/06 02:09 PM
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...no matter which installation [(xx)large; gcc/gfortran/ifort] I choose I get segfaults on my opteron platforms with 64-bit Debian or FC 5 or SuSe 10. There are some bugs somewhere but I
can neither find nor fix them. MANY thanks in advance for further assistance !
(It is somewhat surprising for me as there are already benchmark comparisons published with older charmm versions for Opteron platforms so that there should be a way to install it on AMD64 platforms...)

best regards, David

Re: NO stable c32b2 installation for AMD Opteron possible ?!?
greenhorn #10504 07/17/06 03:54 PM
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rmv Online Content
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Those benchmarks may be in 32-bit mode; the g77 compiler isn't suitable for true 64-bit usage. Consider a good commercial compiler such as Intel or Pathscale.


Rick Venable
computational chemist


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