Re: [gmx-users] compile 2016-beta2 failed

[Justin Lemkul]

On 6/17/16 4:15 PM, Albert wrote:

HI Mark:

But in my machine, all the file from cuda-7.5 development package has been
installed.



Have you tried compiling without -j32?  In my experience, trying to use too many 
cores to compile leads to unpredictable failures, like files failing to be read, 
objects not being compiled fully, etc leading to cryptic errors.


-Justin


thanks again.

On 06/17/2016 10:03 PM, Mark Abraham wrote:

Hi,

My earlier comments all stand - you need a working cuda compilation
environment, and the people to help you do that are the people who
installed it:-)

Mark




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] compile 2016-beta2 failed

[Mark Abraham]

Hi,

That's just one part of the puzzle, since you're also trying to use icc and
MPI.

Mark

On Fri, Jun 17, 2016 at 10:16 PM Albert  wrote:

> HI Mark:
>
> But in my machine, all the file from cuda-7.5 development package has
> been installed.
>
> thanks again.
>
> On 06/17/2016 10:03 PM, Mark Abraham wrote:
> > Hi,
> >
> > My earlier comments all stand - you need a working cuda compilation
> > environment, and the people to help you do that are the people who
> > installed it:-)
> >
> > Mark
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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Re: [gmx-users] compile 2016-beta2 failed

[Albert]

HI Mark:

But in my machine, all the file from cuda-7.5 development package has 
been installed.


thanks again.

On 06/17/2016 10:03 PM, Mark Abraham wrote:

Hi,

My earlier comments all stand - you need a working cuda compilation
environment, and the people to help you do that are the people who
installed it:-)

Mark


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Re: [gmx-users] compile 2016-beta2 failed

[Mark Abraham]

Hi,

My earlier comments all stand - you need a working cuda compilation
environment, and the people to help you do that are the people who
installed it :-)

Mark

On Fri, Jun 17, 2016 at 9:52 PM Albert  wrote:

> Thanks a lot for such comments.
>
> I specified the path of cicc in my .bashrc as the following:
>
> export PATH=/opt/common/cuda-7.5/nvvm/bin:$PATH
>
> Then compiled it again
>
> cmake .. -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs/2016-beta2
> -DGMX_GPU=ON -DGMX_MPI=ON -DCUDA_TOOLKIT_ROOT_DIR=/opt/common/cuda-7.5
>
> make -j32
>
> but it still failed:
>
>
> [  1%] Built target view_objlib
> [  1%] Built target mdrun_objlib
> error in open: error in open: error in open: error in open:
>
> /opt/common/cuda-7.5/bin/../nvvm/libdevice/libdevice.compute_20.10.bc/opt/common/cuda-7.5/bin/../nvvm/libdevice/libdevice.compute_20.10.bc
> /opt/common/cuda-7.5/bin/../nvvm/libdevice/libdevice.compute_20.10.bc
> /opt/common/cuda-7.5/bin/../nvvm/libdevice/libdevice.compute_20.10.bc
>
> No such file or directoryNo such file or directoryNo such file or directory
> ake[2]: ***
>
> [src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_cudautils.cu.o]
> Error 1
> make[2]: ***
>
> [src/gromacs/CMakeFiles/libgromacs.dir/utility/./libgromacs_generated_cuda_version_information.cu.o]
> Error 1
> CMake Error at libgromacs_generated_pmalloc_cuda.cu.o.cmake:260 (message):
>Error generating file
>
> /home/albert/Downloads/gromacs-2016-beta2/build/src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_pmalloc_cuda.cu.o
>
>
> make[2]: ***
>
> [src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_pmalloc_cuda.cu.o]
> Error 1
> error in open:
> /opt/common/cuda-7.5/bin/../nvvm/libdevice/libdevice.compute_20.10.bc
> No such file or directory
> CMake Error at libgromacs_generated_nbnxn_cuda.cu.o.cmake:260 (message):
>Error generating file
>
> /home/albert/Downloads/gromacs-2016-beta2/build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda.cu.o
>
>
> make[2]: ***
>
> [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda.cu.o]
> Error 1
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
>
>
>
>
> On 06/17/2016 09:31 PM, Christopher Neale wrote:
> > cicc is a cuda compiler (i.e., nvcc)
>
> --
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Re: [gmx-users] compile 2016-beta2 failed

[Albert]

Thanks a lot for such comments.

I specified the path of cicc in my .bashrc as the following:

export PATH=/opt/common/cuda-7.5/nvvm/bin:$PATH

Then compiled it again

cmake .. -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs/2016-beta2 
-DGMX_GPU=ON -DGMX_MPI=ON -DCUDA_TOOLKIT_ROOT_DIR=/opt/common/cuda-7.5


make -j32

but it still failed:


[  1%] Built target view_objlib
[  1%] Built target mdrun_objlib
error in open: error in open: error in open: error in open: 
/opt/common/cuda-7.5/bin/../nvvm/libdevice/libdevice.compute_20.10.bc/opt/common/cuda-7.5/bin/../nvvm/libdevice/libdevice.compute_20.10.bc

/opt/common/cuda-7.5/bin/../nvvm/libdevice/libdevice.compute_20.10.bc
/opt/common/cuda-7.5/bin/../nvvm/libdevice/libdevice.compute_20.10.bc

No such file or directoryNo such file or directoryNo such file or directory
ake[2]: *** 
[src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_cudautils.cu.o] 
Error 1
make[2]: *** 
[src/gromacs/CMakeFiles/libgromacs.dir/utility/./libgromacs_generated_cuda_version_information.cu.o] 
Error 1

CMake Error at libgromacs_generated_pmalloc_cuda.cu.o.cmake:260 (message):
  Error generating file
/home/albert/Downloads/gromacs-2016-beta2/build/src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_pmalloc_cuda.cu.o


make[2]: *** 
[src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_pmalloc_cuda.cu.o] 
Error 1
error in open: 
/opt/common/cuda-7.5/bin/../nvvm/libdevice/libdevice.compute_20.10.bc

No such file or directory
CMake Error at libgromacs_generated_nbnxn_cuda.cu.o.cmake:260 (message):
  Error generating file
/home/albert/Downloads/gromacs-2016-beta2/build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda.cu.o


make[2]: *** 
[src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda.cu.o] 
Error 1

make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2





On 06/17/2016 09:31 PM, Christopher Neale wrote:

cicc is a cuda compiler (i.e., nvcc)


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Re: [gmx-users] compile 2016-beta2 failed

[Christopher Neale]

cicc is a cuda compiler (i.e., nvcc)


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Albert 
<mailmd2...@gmail.com>
Sent: 17 June 2016 14:55:02
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] compile 2016-beta2 failed

HEllo Mark:

Thanks a lot for the reply.

I replied Gromacs with the following command line:

cmake .. -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs/2016-beta2
-DGMX_GPU=ON -DGMX_MPI=ON -DCUDA_TOOLKIT_ROOT_DIR=/opt/common/cuda-7.5

make -j32


But it still failed with messages:

Building NVCC (Device) object
src/gromacs/CMakeFiles/libgromacs.dir/utility/./libgromacs_generated_cuda_version_information.cu.o
[  1%] Built target view_objlib
[  1%] Built target mdrun_objlib
sh: 1: cicc: not found
sh: 1: cicc: not found
CMake Error at libgromacs_generated_pmalloc_cuda.cu.o.cmake:260 (message):
   Error generating file
/home/albert/Downloads/gromacs-2016-beta2/build/src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_pmalloc_cuda.cu.o
make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_pmalloc_cuda.cu.o]
Error 1


I don't know what is cicc.? Do you have any suggestions?

thanks a lot

Albert


On 06/17/2016 08:50 PM, Mark Abraham wrote:
> Hi,
>
> Whatever cicc is, you look like you've changed the environment between when
> you started make and continued it. That's probably unwise. Also you made a
> spelling error in your install prefix, which you probably want to fix.
>
> Mark

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Re: [gmx-users] compile 2016-beta2 failed

[Mark Abraham]

Hi,

You're going to need to talk to your cluster admin about how to get a
working CUDA compilation setup. Once you have that, GROMACS will compile.

Mark

On Fri, Jun 17, 2016 at 8:56 PM Albert  wrote:

> HEllo Mark:
>
> Thanks a lot for the reply.
>
> I replied Gromacs with the following command line:
>
> cmake .. -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs/2016-beta2
> -DGMX_GPU=ON -DGMX_MPI=ON -DCUDA_TOOLKIT_ROOT_DIR=/opt/common/cuda-7.5
>
> make -j32
>
>
> But it still failed with messages:
>
> Building NVCC (Device) object
>
> src/gromacs/CMakeFiles/libgromacs.dir/utility/./libgromacs_generated_cuda_version_information.cu.o
> [  1%] Built target view_objlib
> [  1%] Built target mdrun_objlib
> sh: 1: cicc: not found
> sh: 1: cicc: not found
> CMake Error at libgromacs_generated_pmalloc_cuda.cu.o.cmake:260 (message):
>Error generating file
>
> /home/albert/Downloads/gromacs-2016-beta2/build/src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_pmalloc_cuda.cu.o
> make[2]: ***
>
> [src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_pmalloc_cuda.cu.o]
> Error 1
>
>
> I don't know what is cicc.? Do you have any suggestions?
>
> thanks a lot
>
> Albert
>
>
> On 06/17/2016 08:50 PM, Mark Abraham wrote:
> > Hi,
> >
> > Whatever cicc is, you look like you've changed the environment between
> when
> > you started make and continued it. That's probably unwise. Also you made
> a
> > spelling error in your install prefix, which you probably want to fix.
> >
> > Mark
>
> --
> Gromacs Users mailing list
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Re: [gmx-users] compile 2016-beta2 failed

[Albert]

HEllo Mark:

Thanks a lot for the reply.

I replied Gromacs with the following command line:

cmake .. -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs/2016-beta2 
-DGMX_GPU=ON -DGMX_MPI=ON -DCUDA_TOOLKIT_ROOT_DIR=/opt/common/cuda-7.5


make -j32


But it still failed with messages:

Building NVCC (Device) object 
src/gromacs/CMakeFiles/libgromacs.dir/utility/./libgromacs_generated_cuda_version_information.cu.o

[  1%] Built target view_objlib
[  1%] Built target mdrun_objlib
sh: 1: cicc: not found
sh: 1: cicc: not found
CMake Error at libgromacs_generated_pmalloc_cuda.cu.o.cmake:260 (message):
  Error generating file
/home/albert/Downloads/gromacs-2016-beta2/build/src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_pmalloc_cuda.cu.o
make[2]: *** 
[src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_pmalloc_cuda.cu.o] 
Error 1



I don't know what is cicc.? Do you have any suggestions?

thanks a lot

Albert


On 06/17/2016 08:50 PM, Mark Abraham wrote:

Hi,

Whatever cicc is, you look like you've changed the environment between when
you started make and continued it. That's probably unwise. Also you made a
spelling error in your install prefix, which you probably want to fix.

Mark


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Re: [gmx-users] compile 2016-beta2 failed

[Mark Abraham]

Hi,

Whatever cicc is, you look like you've changed the environment between when
you started make and continued it. That's probably unwise. Also you made a
spelling error in your install prefix, which you probably want to fix.

Mark

On Fri, Jun 17, 2016 at 8:38 PM Albert  wrote:

> Hello:
>
> I am trying to use the following command line to compile Gromacs-2016
> beta2:
>
> CMAKE_PREFIX_PATH=/home/albert/install/gromacs/fftw-3.3.4 cmake ..
> -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs/romacs-2016-beta2
> -DGMX_GPU=ON -DGMX_MPI=ON
>
> make -j32
>
> but the make step failed with messages:
>
>
> sh: 1: cicc: not found
> sh: 1: cicc: not found
> sh: 1: cicc: not found
> sh: 1: cicc: not found
> CMake Error at
> libgromacs_generated_cuda_version_information.cu.o.cmake:260 (message):
>Error generating file
>
> /home/albert/Downloads/gromacs-2016-beta2/build/src/gromacs/CMakeFiles/libgromacs.dir/utility/./libgromacs_generated_cuda_version_information.cu.o
> make[2]: ***
>
> [src/gromacs/CMakeFiles/libgromacs.dir/utility/./libgromacs_generated_cuda_version_information.cu.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs
> CMake Error at libgromacs_generated_cudautils.cu.o.cmake:260 (message):
>Error generating file
>
> /home/albert/Downloads/gromacs-2016-beta2/build/src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_cudautils.cu.o
>
>
>
> I am just wondering how to solve the problem?
>
> Thanks a lot
>
> Albert
>
> --
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