AW: compiling charm++ Error: can not find mpi library

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Sep 27 2012 - 08:14:57 CDT

If it works, what's the problem then?

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Thomas Evangelidis
Gesendet: Donnerstag, 27. September 2012 09:00
An: Namd Mailing List
Betreff: Re: namd-l: compiling charm++ Error: can not find mpi library

 

Hi Norman,

Thanks for your comment. From what I understand you mean not to use the icc
flag since the mpich2 compilation has been done with the icc compiler,
correct?

It is worth-mentioning that although icc flag leads to error ifort does not,
namely the following command line works:

./build charm++ mpi-linux-x86_64 --basedir /usr/local/mpich-1.4.1p1_icc
ifort -O

but this one doesn't:

./build charm++ mpi-linux-x86_64 --basedir /usr/local/mpich-1.4.1p1_icc icc
ifort -O

Thanks,
Thomas

On 27 September 2012 09:46, Norman Geist <norman.geist_at_uni-greifswald.de>
wrote:

Hi Thomas,

 

while compiling the mpi, it will create some wrapper compilers, for example
mpicc which will call the compiler you used for the mpi build, so in this
case icc, and will pass all required librarys by default, so you don't have
to care about this anymore. That's the trick, so just use the mpicc now.

 

Good luck

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Thomas Evangelidis

Gesendet: Donnerstag, 27. September 2012 00:15
An: namd-l

Betreff: namd-l: compiling charm++ Error: can not find mpi library

 

Greetings,

I have compiled mpich-1.4.1p1 using the Intel compilers. When I try to
compile charmm++ the following command line completes successfully:

./build charm++ mpi-linux-x86_64 -j8 --basedir /usr/local/mpich-1.4.1p1_icc
-O

but when I add the icc flag to use the Intel compiler I get:

checking "whether build on MPI"... "yes"
checking "whether need to specify MPI library"... "yes"
checking "whether -lmpich"... "no"
checking "whether -lmpi"... "no"
Error: can not find mpi library
*** Please find detailed output in charmconfig.out ***

My charmmconfig.out has the following stack trace:

### whether -lmpich
#include "mpi.h"
int main(int argc, char **argv)
{
  MPI_Init(&argc, &argv);
}
icpc -fpic -I../include -I. -fno-stack-protector
-I/usr/local/mpich-1.4.1p1_icc/include -c test.cpp -o test.o -lmpich
icpc -shared-intel -o testlink test.o -L/usr/local/mpich-1.4.1p1_icc/lib
-lmpich
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(init.o): In function `MPI_Init':
init.c:(.text+0x6e): undefined reference to `MPL_env2str'
init.c:(.text+0x268): undefined reference to `MPL_env2bool'
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(initthread.o): In function
`MPI_Init_thread':
initthread.c:(.text+0x113): undefined reference to `MPL_env2bool'
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(mpiu_thread.o): In function
`MPIU_Thread_create':
mpiu_thread.c:(.text+0x5f): undefined reference to `pthread_create'
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(param_vals.o): In function
`MPIR_Param_init_params':
param_vals.c:(.text+0x10): undefined reference to `MPL_env2int'
param_vals.c:(.text+0x28): undefined reference to `MPL_env2int'
param_vals.c:(.text+0x40): undefined reference to `MPL_env2int'
param_vals.c:(.text+0x58): undefined reference to `MPL_env2int'
param_vals.c:(.text+0x70): undefined reference to `MPL_env2int'
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(param_vals.o):param_vals.c:(.tex
t+0x88): more undefined references to `MPL_env2int' follow
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(param_vals.o): In function
`MPIR_Param_init_params':
param_vals.c:(.text+0x328): undefined reference to `MPL_env2bool'
param_vals.c:(.text+0x340): undefined reference to `MPL_env2bool'
param_vals.c:(.text+0x358): undefined reference to `MPL_env2bool'
param_vals.c:(.text+0x370): undefined reference to `MPL_env2bool'
param_vals.c:(.text+0x388): undefined reference to `MPL_env2bool'
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(param_vals.o):param_vals.c:(.tex
t+0x3a0): more undefined references to `MPL_env2bool' follow
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(param_vals.o): In function
`MPIR_Param_init_params':
param_vals.c:(.text+0x448): undefined reference to `MPL_env2int'
param_vals.c:(.text+0x460): undefined reference to `MPL_env2int'
param_vals.c:(.text+0x478): undefined reference to `MPL_env2bool'
param_vals.c:(.text+0x490): undefined reference to `MPL_env2bool'
param_vals.c:(.text+0x4a8): undefined reference to `MPL_env2bool'
param_vals.c:(.text+0x4c0): undefined reference to `MPL_env2bool'
param_vals.c:(.text+0x4d8): undefined reference to `MPL_env2bool'
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(param_vals.o):param_vals.c:(.tex
t+0x4f0): more undefined references to `MPL_env2bool' follow
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(param_vals.o): In function
`MPIR_Param_init_params':
param_vals.c:(.text+0x508): undefined reference to `MPL_env2int'
param_vals.c:(.text+0x520): undefined reference to `MPL_env2int'
param_vals.c:(.text+0x538): undefined reference to `MPL_env2int'
param_vals.c:(.text+0x550): undefined reference to `MPL_env2int'
param_vals.c:(.text+0x568): undefined reference to `MPL_env2str'
param_vals.c:(.text+0x580): undefined reference to `MPL_env2str'
param_vals.c:(.text+0x598): undefined reference to `MPL_env2str'
param_vals.c:(.text+0x5b0): undefined reference to `MPL_env2str'
param_vals.c:(.text+0x5c8): undefined reference to `MPL_env2str'
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(param_vals.o):param_vals.c:(.tex
t+0x5e0): more undefined references to `MPL_env2str' follow
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(param_vals.o): In function
`MPIR_Param_init_params':
param_vals.c:(.text+0x5f8): undefined reference to `MPL_env2int'
param_vals.c:(.text+0x610): undefined reference to `MPL_env2int'
param_vals.c:(.text+0x628): undefined reference to `MPL_env2bool'
param_vals.c:(.text+0x640): undefined reference to `MPL_env2bool'
param_vals.c:(.text+0x658): undefined reference to `MPL_env2bool'
param_vals.c:(.text+0x670): undefined reference to `MPL_env2bool'
param_vals.c:(.text+0x688): undefined reference to `MPL_env2bool'
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(param_vals.o):param_vals.c:(.tex
t+0x6a0): more undefined references to `MPL_env2bool' follow
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(param_vals.o): In function
`MPIR_Param_init_params':
param_vals.c:(.text+0x6ed): undefined reference to `MPL_env2range'
param_vals.c:(.text+0x70a): undefined reference to `MPL_env2range'
param_vals.c:(.text+0x727): undefined reference to `MPL_env2range'
param_vals.c:(.text+0x740): undefined reference to `MPL_env2range'
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(mpid_init.o): In function
`MPID_Init':
mpid_init.c:(.text+0x172): undefined reference to `MPL_env2bool'
/usr/local/mpich-1.4.1p1_icc/lib/libmpich.a(mpid_vc.o): In function
`MPIDI_Populate_vc_node_ids':
mpid_vc.c:(.text+0xcd0): undefined reference to `MPL_env2int'
mpid_vc.c:(.text+0xce2): undefined reference to `MPL_env2int'

Any idea why this is happening?

Thomas

-- 
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
          tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
 
 
-- 
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
          tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
 
 

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