From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Thu Sep 27 2012 - 02:00:24 CDT
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:(.text+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:(.text+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:(.text+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:(.text+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:(.text+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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