AMBER Archive (2006)

Subject: AMBER: Amber8 parallel compilation problems on EM64T system

From: HL Eastwood (s0237717_at_sms.ed.ac.uk)
Date: Thu Feb 02 2006 - 13:32:32 CST

Dear Amber users

I have been trying to compile the parallel version of amber but nothing
I do seems to work. Here is how I configured it:

general info:
linux system: suse 9.2
processor: Xeon EM64T, 2.8 GHZ
c-compiler: l_cce_pc_8.1.026
f-compiler (64bit compatible): Version 8.1.046
LAMHOME + AMBERHOME set within .bashrc

LAM:
$ export CXX=icc
$ export FC=ifort
$ export CFLAGS=-static
$ export CXXFLAGS=-static
$ export FFLAGS=-static

(I also tried setting CC=icc too but this resulted in lam compilation
errors for mpif77 and laminfo - mpif77 appears to be required by Sander)

$ make
$ make install

(NB lam makes fine and tests fine across all nodes)

AMBER
$ ./configure -lam ifort
$ make parallel

when this failed I tried all possible combinations for the parallel compile:
$ ./configure -lam -static ifort
$ ./configure -lam -ia64_ifort ifort
$ ./configure -lam -ia64_ifort -static ifort

(NB make serial works just fine)

Every time i invoke "make parallel" I get an output something along the
lines of:

/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0xa0): In function
`malloc_atfork':
: undefined reference to `pthread_getspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x15c): In function `free_atfork':
: undefined reference to `pthread_getspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x21e): In function
`ptmalloc_lock_all':
: undefined reference to `pthread_getspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x23a): In function
`ptmalloc_lock_all':
: undefined reference to `pthread_setspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x25a): In function
`ptmalloc_unlock_all':
: undefined reference to `pthread_setspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x3b6): In function
`ptmalloc_init':
: undefined reference to `pthread_key_create'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x3c8): In function
`ptmalloc_init':
: undefined reference to `pthread_setspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x3e2): In function
`ptmalloc_init':
: undefined reference to `pthread_atfork'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x89a): In function `arena_get2':
: undefined reference to `pthread_mutex_trylock'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x8ba): In function `arena_get2':
: undefined reference to `pthread_mutex_trylock'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x8f1): In function `arena_get2':
: undefined reference to `pthread_setspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x94d): In function `arena_get2':
: undefined reference to `pthread_setspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x1f66): In function `malloc':
: undefined reference to `pthread_getspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x1f76): In function `malloc':
: undefined reference to `pthread_mutex_trylock'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x2202): In function `realloc':
: undefined reference to `pthread_setspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x229a): In function `memalign':
: undefined reference to `pthread_getspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x22aa): In function `memalign':
: undefined reference to `pthread_mutex_trylock'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x23a3): In function `valloc':
: undefined reference to `pthread_getspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x23b3): In function `valloc':
: undefined reference to `pthread_mutex_trylock'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x2419): In function `pvalloc':
: undefined reference to `pthread_getspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x2429): In function `pvalloc':
: undefined reference to `pthread_mutex_trylock'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x2497): In function `calloc':
: undefined reference to `pthread_getspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x24a7): In function `calloc':
: undefined reference to `pthread_mutex_trylock'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x26c9): In function
`independent_calloc':
: undefined reference to `pthread_getspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x26d9): In function
`independent_calloc':
: undefined reference to `pthread_mutex_trylock'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x2741): In function
`independent_comalloc':
: undefined reference to `pthread_getspecific'
/opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0x2751): In function
`independent_comalloc':
: undefined reference to `pthread_mutex_trylock'
/opt/lam-7.1.1/lib/liblam.a(lammutex.o)(.text+0x89): In function
`lam_mutex_trylock':
: undefined reference to `pthread_mutex_trylock'
/opt/lam-7.1.1/lib/liblam.a(lamthreads.o)(.text+0xd): In function
`lam_thread_create':
: undefined reference to `pthread_create'
/opt/lam-7.1.1/lib/liblam.a(lamthreads.o)(.text+0x1e): In function
`lam_thread_join':
: undefined reference to `pthread_join'
make[1]: *** [sander] Error 1
make[1]: Leaving directory `/opt/amber8/src/sander'
make: *** [parallel] Error 2

Please help, my sanity is evaporating.

many thanks

Hayden Eastwood

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