Problem installing mpi-enabled Plumed2-2.1-hrex

[Abhi Acharya]

Hello,

Although the mpi-disabled plumed installed without hassle, I am not able to install with MPI. I have installed OPEN-MPI version 1.8.2 and that works fine.

So, essentially I ran the configure step as:

./configure --prefix=/usr/local/plumed

The Output seemed fine, except for few excerpts which i feel are important here:

checking for mpic++... mpic++

checking whether the C++ compiler works... yes

.....

checking for suffix of object files... o

checking whether we are using the GNU C++ compiler... yes

checking whether mpic++ accepts -g... yes

......

checking mpi.h usability... yes

checking mpi.h presence... yes

checking for mpi.h... yes

checking for MPI_Init... yes

......

configure: PLUMED seems to be configured properly!

configure: **************************

configure: I will now check if C++ objects can be linked by C/Fortran compilers

configure: This is relevant if you want to use plumed patch --static on a non-C++ code

checking whether C can link a C++ object... no

checking whether C can link a C++ object with library -lstdc++... no

checking whether C can link a C++ object with library -lc++... no

configure: WARNING: You might have problems linking C programs.

configure: WARNING: Please add c++ library to LIBS - e.g. LIBS=-lstdc++

checking whether FORTRAN can link a C++ object... no

checking whether FORTRAN can link a C++ object with library -lstdc++... no

checking whether FORTRAN can link a C++ object with library -lc++... no

configure: WARNING: You might have problems linking FORTRAN programs.

configure: WARNING: Please add c++ library to LIBS - e.g. LIBS=-lstdc++

configure: **** PLUMED will be installed using prefix /usr/local/plumed

configure: **** You can change this later setting PLUMED_PREFIX environment variable before installing

configure: **** Executable will be named 'plumed'

configure: **** To add a suffix to this name, set PLUMED_LIBSUFFIX environment variable before installing

configure: creating ./config.status

config.status: creating Makefile.conf

config.status: creating sourceme.sh

Note: I am quite sure the above warnings regarding lstdc++ were also visible during the previous installation without MPI, but plumed (same version) was successfully patched with gromacs-4.6.7. 

Anyways, after this step there is a problem.

On giving the command 'make', i get a long output which completes normally, but after 'sudo make install' there is an error:

 make[5]: mpic++: Command not found

make[5]: *** [/usr/local/plumed/lib/plumed//src/lib/plumed] Error 127

make[5]: Leaving directory `/home/abhi/Downloads/plumed2-2.1-hrex/src/lib'

make[4]: *** [all] Error 2

make[4]: Leaving directory `/home/abhi/Downloads/plumed2-2.1-hrex/src/lib'

make[3]: *** [install-do] Error 2

make[3]: Leaving directory `/home/abhi/Downloads/plumed2-2.1-hrex/src/lib'

make[2]: *** [install] Error 2

make[2]: Leaving directory `/home/abhi/Downloads/plumed2-2.1-hrex/src/lib'

make[1]: *** [install] Error 2

make[1]: Leaving directory `/home/abhi/Downloads/plumed2-2.1-hrex/src'

make: *** [install] Error 2

Incidentally, after './configure' step I had also tried running "sudo make", and in this case it stops within seconds with the same error (but, of course this time in the penultimate step).

make[6]: mpic++: Command not found

make[6]: *** [Analysis.o] Error 127

make[6]: Leaving directory `/home/abhi/Downloads/plumed2-2.1-hrex-2/src/analysis'

make[5]: *** [../analysis] Error 2

make[5]: Leaving directory `/home/abhi/Downloads/plumed2-2.1-hrex-2/src/lib'

make[4]: *** [dirs] Error 2

make[4]: Leaving directory `/home/abhi/Downloads/plumed2-2.1-hrex-2/src/lib'

make[3]: *** [all] Error 2

make[3]: Leaving directory `/home/abhi/Downloads/plumed2-2.1-hrex-2/src/lib'

make[2]: *** [lib] Error 2

make[2]: Leaving directory `/home/abhi/Downloads/plumed2-2.1-hrex-2/src'

make[1]: *** [lib] Error 2

make[1]: Leaving directory `/home/abhi/Downloads/plumed2-2.1-hrex-2'

make: *** [all] Error 2

Its beyond me, why such a difference in the output of 'make' and 'sudo make' ? Also, I was also wondering, why the error says mpic++ command not found when the configure step shows it could find mpic++.

Any explanations, as well as troubleshooting would be very helpful.

Regards,

Abhishek

[davide branduardi]

Hi Abhishek, 

I am just guessing...

could it be that when you do sudo then your environment is weeped out and along with that the knowledge of the path to mpic++ ?

D

[Abhi Acharya]

Hello,

I have never encountered such a problem before, but just to see whether that's a possibility, I tried to install gromacs with mpi. I did not face any such problems whatsoever.  Also the said gromacs installation runs properly using mpi processes, so that doesn't seem like a reason.

What do you think?

Regards,

Abhishek

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[Giovanni Bussi]

Hi!

I think the problem is that when you type "make install" PLUMED uses the linker to link a new version of the library file in the correct directory. The reason for relinking is that paths are hardcoded in the library and paths can be decided at install time. Maybe it is not the best choice, but I did not know any other way to hardcode a path in the library and change it at install time.

Try to type:

mpic++

sudo mpic++

If the first succeeds and the second fails, the root user in your system (or better, your user when running within sudo) has no access to mpic++ compiler. I do not know if this is a common situation. Maybe you installed mpi compilers locally to your user?

Possible solutions:

1. "sudo -E" instead of "sudo" could work possibly if it is enabled on your system.

2. Find another way to change the environment loaded by sudo

3. As a last resort, do not install PLUMED but use it from the compilation directory. It should be completely functional.

Let us know if you can fix the problem,

regards,

Giovanni

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[Abhi Acharya]

Dear Dr. Giovanni,

Sorry for the delay. Indeed, when i type "sudo mpic++" it says command not found (becoz it was installed in /usr/local/openmp folder)

So, I had to add the path of OPEN-MPI install to the path field in sudoer.tmp file. 

The installation was completed :)

Thank you to you as well as Davide.

Regards,

Abhishek

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[ychu...@gmail.com]

Hi, 

I have the same problem, but cannot find the sudoer.tmp file. Then how can I solve this problem?

Thanks,

Yuanchao

在 2014年9月18日星期四 UTC-4上午10:58:09，Abhi写道：

[Abhishek Acharya]

Which OS are you using? This problem was encountered way back when I was trying to install on a ubuntu 12.04. Normally, sudoer file is located in /etc/sudoer. You can edit it using visudo editor and add the path to you MPI compiler.

Abhishek

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[Yuan-Chao Hu]

Hi,

I use bash in Win10. The version is Ubuntu 16.04.3. There is no sudoer.tmp under /etc/sudoers but there are sudoers and sudoers.d folder. Should I create the new file? How can I include it in the MPI compiler? Thanks

Yuanchao

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Department of Mechanical Engineering & Materials Science

Yale University

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[Abhishek Acharya]

Are you using a virtual environment on win10? I am afraid I have not used ubuntu in that setup, so I can't comment on the issue you are facing. Perhaps you should post about the problem with sudoer file somewhere else like stackoverflow maybe.

Abhishek

[Yuan-Chao Hu]

Hi, 

I think so. Thanks for your nice reply.

Best,

Yuanchao

On Mon, Aug 13, 2018 at 1:57 AM Abhishek Acharya <abhi117...@gmail.com> wrote:

Are you using a virtual environment on win10? I am afraid I have not used ubuntu in that setup, so I can't comment on the issue you are facing. Perhaps you should post about the problem with sudoer file somewhere else like stackoverflow maybe.

Abhishek

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