[gmx-users] installation problem

[banijamali_fs]

Hi there, 

I want to install gromacs-5.0.7 with this installation guide,

tar xfz gromacs-5.0.7.tar.gz
cd gromacs-5.0.7
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

after running all of these commands, I type gmx to know that if this
program is correctly installed and to know
that where this program installed, but I receive this error:
gmx:error while loading shared libraries: libgromacs.so.0: cannot open
shared object file: NO such file or 
directory, I don't know what should I do? I'm totally confused, I try
many ways, but I didn't get result, please
 help me with this problem.
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Re: [gmx-users] installation problem

[João Henriques]

This is completely vague. Please report what the actual error is and then
people might be able to help.

J

On Mon, Feb 19, 2018 at 9:43 AM, banijamali_fs 
wrote:

> Hi there,
>
> unfortunately I uninstall the gromacs program from my PC and I couldn't
> install it again with so many ways that I tested, I want to ask you that
> in which step I made mistake that I can't install it.
>
> these are the steps that I've done but I didn't get the suitable result.
>
> tar xfz gromacs-5.0.7.tar.gz
> cd gromacs-5.0.7
> mkdir build
> cd build
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> make
> make check
> sudo make install
> source /usr/local/gromacs/bin/GMXRC
>
> I would be vary thankful if anybody help me.
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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[gmx-users] installation problem

[banijamali_fs]

Hi there, 

unfortunately I uninstall the gromacs program from my PC and I couldn't
install it again with so many ways that I tested, I want to ask you that
in which step I made mistake that I can't install it. 

these are the steps that I've done but I didn't get the suitable result.

tar xfz gromacs-5.0.7.tar.gz
cd gromacs-5.0.7
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

I would be vary thankful if anybody help me.
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Re: [gmx-users] Installation Problem... No command 'gmx' found

[Md. Imrul Reza Shishir]

Thanks everyone. For your quick reply and support.

On Thu, Apr 21, 2016 at 10:37 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/21/16 9:35 AM, Sotirios Dionysios I. Papadatos wrote:
>
>> Hi, in my case gmx is only needed for certain commands. For example
>> pdb2gmx is working if I use it solo, not with gmx. It's worth a shot.
>>
>>
> This is true for versions in the 5.0.x series; they can be called via gmx
> or through the old syntax without it because the commands are all installed
> as links to gmx.  In 5.1.x this will not work; gmx/gmx_mpi (depending on
> the installation) is mandatory.
>
> -Justin
>
>
> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Email
>> Gmail Pribadi <hus...@gmail.com>
>> Sent: Thursday, April 21, 2016 9:18 AM
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Installation Problem... No command 'gmx' found
>>
>> Hi,
>>
>> Try gmx [command] . Ex. gmx mdrun -option
>>
>> Regards,
>>
>>
>> Husen
>>
>> On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote:
>>>
>>> Hi,
>>>
>>> Try gmx_mpi.
>>>
>>> Regards
>>> Terry
>>>
>>>
>>> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir <
>>>> imrul.reza.shis...@gmail.com> wrote:
>>>>
>>>> Dear all user
>>>>
>>>> I install gromacs in my laptop its perfectly ok. But i have problem to
>>>> install in my desktop there i face problem.
>>>> In my desktop i want to compile with cuda accelerator and MPI option. I
>>>> install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
>>>> this driver is ok.
>>>>
>>>> For gromacs i run this installation command.
>>>>
>>>> tar -xzvf gromacs-5.1.2.tar.gz
>>>> cd gromacs-5.1.2.tar.gz
>>>> mkdir build
>>>> cd build
>>>> CMAKE  -DGMX_BUILD_OWN_FFTW=on
>>>> -DGMX_GPU=on
>>>> -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
>>>> make -j16
>>>> make check
>>>> sudo make install -j16
>>>>
>>>> source /usr/local/gromacs/bin/GMXRC
>>>>
>>>> In the installation procedure i dont find any error. All 26 test
>>>> completed
>>>> without error.
>>>>
>>>> But when i try to run "gmx or gmx help"
>>>>
>>>> There is error no command gmx found. I need your guidance.
>>>>
>>>> Best Regards
>>>>
>>>> --
>>>> *Md Imrul Reza Shishir*
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
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>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>>
> --
> ==
>
> 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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> posting!
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
*Md Imrul Reza Shishir*
Master Student
*Inha University*
*CRC for NanoCellulose Future Composites*
36 Getbeol-ro, Yeonsu-gu
Incheon 21999
South Korea
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Re: [gmx-users] Installation Problem... No command 'gmx' found

[Justin Lemkul]

On 4/21/16 9:35 AM, Sotirios Dionysios I. Papadatos wrote:

Hi, in my case gmx is only needed for certain commands. For example pdb2gmx is 
working if I use it solo, not with gmx. It's worth a shot.



This is true for versions in the 5.0.x series; they can be called via gmx or 
through the old syntax without it because the commands are all installed as 
links to gmx.  In 5.1.x this will not work; gmx/gmx_mpi (depending on the 
installation) is mandatory.


-Justin



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Email Gmail Pribadi 
<hus...@gmail.com>
Sent: Thursday, April 21, 2016 9:18 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Installation Problem... No command 'gmx' found

Hi,

Try gmx [command] . Ex. gmx mdrun -option

Regards,


Husen


On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote:

Hi,

Try gmx_mpi.

Regards
Terry



On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir 
<imrul.reza.shis...@gmail.com> wrote:

Dear all user

I install gromacs in my laptop its perfectly ok. But i have problem to
install in my desktop there i face problem.
In my desktop i want to compile with cuda accelerator and MPI option. I
install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
this driver is ok.

For gromacs i run this installation command.

tar -xzvf gromacs-5.1.2.tar.gz
cd gromacs-5.1.2.tar.gz
mkdir build
cd build
CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
-DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
make -j16
make check
sudo make install -j16

source /usr/local/gromacs/bin/GMXRC

In the installation procedure i dont find any error. All 26 test completed
without error.

But when i try to run "gmx or gmx help"

There is error no command gmx found. I need your guidance.

Best Regards

--
*Md Imrul Reza Shishir*
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--
==

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] Installation Problem... No command 'gmx' found

[Sotirios Dionysios I. Papadatos]

Hi, in my case gmx is only needed for certain commands. For example pdb2gmx is 
working if I use it solo, not with gmx. It's worth a shot.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Email Gmail 
Pribadi <hus...@gmail.com>
Sent: Thursday, April 21, 2016 9:18 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Installation Problem... No command 'gmx' found

Hi,

Try gmx [command] . Ex. gmx mdrun -option

Regards,


Husen

> On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote:
>
> Hi,
>
> Try gmx_mpi.
>
> Regards
> Terry
>
>
>> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir 
>> <imrul.reza.shis...@gmail.com> wrote:
>>
>> Dear all user
>>
>> I install gromacs in my laptop its perfectly ok. But i have problem to
>> install in my desktop there i face problem.
>> In my desktop i want to compile with cuda accelerator and MPI option. I
>> install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
>> this driver is ok.
>>
>> For gromacs i run this installation command.
>>
>> tar -xzvf gromacs-5.1.2.tar.gz
>> cd gromacs-5.1.2.tar.gz
>> mkdir build
>> cd build
>> CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
>> -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
>> make -j16
>> make check
>> sudo make install -j16
>>
>> source /usr/local/gromacs/bin/GMXRC
>>
>> In the installation procedure i dont find any error. All 26 test completed
>> without error.
>>
>> But when i try to run "gmx or gmx help"
>>
>> There is error no command gmx found. I need your guidance.
>>
>> Best Regards
>>
>> --
>> *Md Imrul Reza Shishir*
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
>> mail to gmx-users-requ...@gromacs.org.
> --
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>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
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> mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Installation Problem... No command 'gmx' found

[Email Gmail Pribadi]

Hi,

Try gmx [command] . Ex. gmx mdrun -option

Regards,


Husen

> On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote:
> 
> Hi, 
> 
> Try gmx_mpi.
> 
> Regards
> Terry
> 
> 
>> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir 
>>  wrote:
>> 
>> Dear all user
>> 
>> I install gromacs in my laptop its perfectly ok. But i have problem to
>> install in my desktop there i face problem.
>> In my desktop i want to compile with cuda accelerator and MPI option. I
>> install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
>> this driver is ok.
>> 
>> For gromacs i run this installation command.
>> 
>> tar -xzvf gromacs-5.1.2.tar.gz
>> cd gromacs-5.1.2.tar.gz
>> mkdir build
>> cd build
>> CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
>> -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
>> make -j16
>> make check
>> sudo make install -j16
>> 
>> source /usr/local/gromacs/bin/GMXRC
>> 
>> In the installation procedure i dont find any error. All 26 test completed
>> without error.
>> 
>> But when i try to run "gmx or gmx help"
>> 
>> There is error no command gmx found. I need your guidance.
>> 
>> Best Regards
>> 
>> -- 
>> *Md Imrul Reza Shishir*
>> -- 
>> Gromacs Users mailing list
>> 
>> * Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
>> mail to gmx-users-requ...@gromacs.org.
> -- 
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> 
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Re: [gmx-users] Installation Problem... No command 'gmx' found

[terrencesun]

Hi, 

Try gmx_mpi.

Regards
Terry


> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir 
>  wrote:
> 
> Dear all user
> 
> I install gromacs in my laptop its perfectly ok. But i have problem to
> install in my desktop there i face problem.
> In my desktop i want to compile with cuda accelerator and MPI option. I
> install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
> this driver is ok.
> 
> For gromacs i run this installation command.
> 
> tar -xzvf gromacs-5.1.2.tar.gz
> cd gromacs-5.1.2.tar.gz
> mkdir build
> cd build
> CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
> -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
> make -j16
> make check
> sudo make install -j16
> 
> source /usr/local/gromacs/bin/GMXRC
> 
> In the installation procedure i dont find any error. All 26 test completed
> without error.
> 
> But when i try to run "gmx or gmx help"
> 
> There is error no command gmx found. I need your guidance.
> 
> Best Regards
> 
> -- 
> *Md Imrul Reza Shishir*
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
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> mail to gmx-users-requ...@gromacs.org.
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[gmx-users] Installation Problem... No command 'gmx' found

[Md. Imrul Reza Shishir]

Dear all user

I install gromacs in my laptop its perfectly ok. But i have problem to
install in my desktop there i face problem.
In my desktop i want to compile with cuda accelerator and MPI option. I
install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
this driver is ok.

For gromacs i run this installation command.

tar -xzvf gromacs-5.1.2.tar.gz
cd gromacs-5.1.2.tar.gz
mkdir build
cd build
CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
-DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
make -j16
make check
sudo make install -j16

source /usr/local/gromacs/bin/GMXRC

In the installation procedure i dont find any error. All 26 test completed
without error.

But when i try to run "gmx or gmx help"

There is error no command gmx found. I need your guidance.

​Best Regards

-- 
*Md Imrul Reza Shishir*
-- 
Gromacs Users mailing list

* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Installation problem

[Mark Abraham]

Hi,

As you have read in the install guide (hint, hint) CUDA and OpenCL support
are mutually exclusive. Your second attempt was clearly run in the same
build directory, so you have not changed your previous choice where OpenCL
was on. Either turn it off, change build directory, or clear the contents
of the build directory.

Mark

On Sun, 14 Feb 2016 15:46 Prof. Eddie  wrote:

> Thanks. I thought it would be better to have ocl as well just in case.
> However, I tried you suggestion:
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON ; make
> and it still have the same error
> [100%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o
> Linking CXX shared library ../../lib/libgromacs.so
> [100%] Built target libgromacs
> [100%] Building CXX object
> share/template/CMakeFiles/template.dir/template.cpp.o
> Linking CXX executable ../../bin/template
> ../../lib/libgromacs.so.1.2.0: undefined reference to
> `clEnqueueBarrierWithWaitList'
> ../../lib/libgromacs.so.1.2.0: undefined reference to
> `clEnqueueMarkerWithWaitList'
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2
>
> I did a make clean first and that didn't help. Thanks for continuing to
> help,
> Eddie
>
> On Sun, Feb 14, 2016 at 7:41 AM, Dr. Eddie  wrote:
>
> > Thanks. I thought it would be better to have ocl as well just in case.
> > However, I tried you suggestion:
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON ; make
> > and it still have the same error
> > [100%] Building C object
> > src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o
> > Linking CXX shared library ../../lib/libgromacs.so
> > [100%] Built target libgromacs
> > [100%] Building CXX object
> > share/template/CMakeFiles/template.dir/template.cpp.o
> > Linking CXX executable ../../bin/template
> > ../../lib/libgromacs.so.1.2.0: undefined reference to
> > `clEnqueueBarrierWithWaitList'
> > ../../lib/libgromacs.so.1.2.0: undefined reference to
> > `clEnqueueMarkerWithWaitList'
> > collect2: error: ld returned 1 exit status
> > make[2]: *** [bin/template] Error 1
> > make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> > make: *** [all] Error 2
> >
> > I did a make clean first and that didn't help.
> >
> > On Sat, Feb 13, 2016 at 12:04 PM, Nikhil Maroli 
> > wrote:
> >
> >> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> >>
> >>
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
> >
> > --
> > Eddie
> >
>
>
>
> --
> _
> Edward Ackad, Ph.D 
> Assistant Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Installation problem

[Prof. Eddie]

Thanks. I thought it would be better to have ocl as well just in case.
However, I tried you suggestion:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON ; make
and it still have the same error
[100%] Building C object
src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o
Linking CXX shared library ../../lib/libgromacs.so
[100%] Built target libgromacs
[100%] Building CXX object
share/template/CMakeFiles/template.dir/template.cpp.o
Linking CXX executable ../../bin/template
../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueBarrierWithWaitList'
../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueMarkerWithWaitList'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2

I did a make clean first and that didn't help. Thanks for continuing to
help,
Eddie

On Sun, Feb 14, 2016 at 7:41 AM, Dr. Eddie  wrote:

> Thanks. I thought it would be better to have ocl as well just in case.
> However, I tried you suggestion:
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON ; make
> and it still have the same error
> [100%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o
> Linking CXX shared library ../../lib/libgromacs.so
> [100%] Built target libgromacs
> [100%] Building CXX object
> share/template/CMakeFiles/template.dir/template.cpp.o
> Linking CXX executable ../../bin/template
> ../../lib/libgromacs.so.1.2.0: undefined reference to
> `clEnqueueBarrierWithWaitList'
> ../../lib/libgromacs.so.1.2.0: undefined reference to
> `clEnqueueMarkerWithWaitList'
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2
>
> I did a make clean first and that didn't help.
>
> On Sat, Feb 13, 2016 at 12:04 PM, Nikhil Maroli 
> wrote:
>
>> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>>
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
> --
> Eddie
>



-- 
_
Edward Ackad, Ph.D 
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390
-- 
Gromacs Users mailing list

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Re: [gmx-users] Installation problem

[Prof. Eddie]

Hi,
The system has a gpu (gtx 590) with cuda libraries installed (I've run namd
on the system). It also has mpi:
mpic++   mpiCCmpiCC.openmpimpicxx   mpiexec
 mpif77   mpif90   mpirun
mpiccmpicc.openmpimpic++.openmpi   mpicxx.openmpi
mpiexec.openmpi  mpif77.openmpi   mpif90.openmpi   mpirun.openmpi

CPU
Architecture:  x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):8
On-line CPU(s) list:   0-7
Thread(s) per core:1
Core(s) per socket:8
Socket(s): 1
NUMA node(s):  2
Vendor ID: AuthenticAMD
CPU family:16
Model: 9
Stepping:  1
CPU MHz:   800.000
BogoMIPS:  4000.02
Virtualization:AMD-V
L1d cache: 64K
L1i cache: 64K
L2 cache:  512K
L3 cache:  5118K
NUMA node0 CPU(s): 0-3
NUMA node1 CPU(s): 4-7

gcc
gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04.1)

The error was about ../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueMarkerWithWaitList'

Any idea what that belongs to? Any other details let me know.
Let me know
Thanks,
Eddie

On Fri, Feb 12, 2016 at 11:26 PM, Nikhil Maroli  wrote:

> Hi,
> What is your system details?Do you have GPU ,if yes CUDA library is
> installed?
> if not please install CUDA library and MPI packages too!
> hope it will fix
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
_
Edward Ackad, Ph.D 
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] Installation problem

[Nikhil Maroli]

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON



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[gmx-users] Installation problem

[Prof. Eddie]

Hi All,
I'm trying to install GROMACS 5.1.2 on ubuntu 14.04 LTS. I used:
cmake .. -DGMX_GPU=on -DGMX_USE_OPENCL=on -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON

Everything went fine, but make ended with:

[100%] Building C object
src/gromacs/CMakeFiles/libgromacs.dir/__/external/thread_mpi/src/once.c.o
[100%] Building C object
src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o
Linking CXX shared library ../../lib/libgromacs.so
[100%] Built target libgromacs
Scanning dependencies of target template
[100%] Building CXX object
share/template/CMakeFiles/template.dir/template.cpp.o
Linking CXX executable ../../bin/template
../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueBarrierWithWaitList'
../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueMarkerWithWaitList'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2
eddie@heartofgold:~/bin/gromacs-5.1.2/build$ ^C
eddie@heartofgold:~/bin/gromacs-5.1.2/build$ make
[  0%] Built target fftwBuild
[100%] Built target libgromacs
Linking CXX executable ../../bin/template
../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueBarrierWithWaitList'
../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueMarkerWithWaitList'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2

Any help would be very welcome! Thanks,
Eddie
-- 
_
Edward Ackad, Ph.D 
Assistant Professor of Physics
Computational Nanophotonics/Biophysics
Southern Illinois University Edwardsville
(618) 650-2390
-- 
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Re: [gmx-users] Installation problem

[Nikhil Maroli]

Hi,
What is your system details?Do you have GPU ,if yes CUDA library is 
installed?
if not please install CUDA library and MPI packages too!
hope it will fix

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[gmx-users] Installation problem

[Nima Soltani]

Hi,

I want to install gromacs 5.0.5 but after issuing this command:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

I encounter the folloeing error:
Downloading: http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz
CMake Error at tests/CMakeLists.txt:57 (message):
  error: downloading
  'http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz' failed

  status_code: 1

  status_string: unsupported protocol

  log: About to connect() to gerrit.gromacs.org port 80 (#0)

Trying 130.237.25.133... connected

  Connected to gerrit.gromacs.org (130.237.25.133) port 80 (#0)

  GET /download/regressiontests-5.0.5.tar.gz HTTP/1.1

  Host: gerrit.gromacs.org

  Accept: */*



  HTTP/1.1 302 Found

  Date: Mon, 06 Jul 2015 09:29:46 GMT

  Server: Apache/2.2.22 (Ubuntu)

  Location:
  https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz

  Vary: Accept-Encoding

  Content-Length: 337

  Content-Type: text/html; charset=iso-8859-1

  Ignoring the response-body

  !DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN

  htmlhead

  title302 Found/title

  /headbody

  h1Found/h1

  pThe document has moved a
  href=
https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz;
https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz
here/a./p


  hr

  addressApache/2.2.22 (Ubuntu) Server at gerrit.gromacs.org Port
  80/address

  /body/html

  Connection #0 to host gerrit.gromacs.org left intact

  Issue another request to this URL:
  'https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz'

  libcurl was built with SSL disabled, https: not supported!

  unsupported protocol

  Closing connection #0

-

what can I do?
does installing another version of Cmake makes any difference ?



Best Regards,
Nima Soltani
--
Graduate Student of Physical Chemistry
Department of Chemistry,
Sharif University of Technology.
=
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Re: [gmx-users] Installation problem

[Mark Abraham]

Hi,

The real problem description is at the end. You are doing the download with
a cmake that relies on curl that relies on libssl and that doesn't support
the boring standard https protocol. Perhaps your operating system is too
old to be useful. You can bypass this and get the tests yourself, following
http://www.gromacs.org/Documentation/Installation_Instructions_5.0#testing-gromacs-for-correctness

Mark

On Mon, 6 Jul 2015 12:31 Nima Soltani nima@gmail.com wrote:

 Hi,

 I want to install gromacs 5.0.5 but after issuing this command:
 cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

 I encounter the folloeing error:
 Downloading:
 http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz
 CMake Error at tests/CMakeLists.txt:57 (message):
   error: downloading
   'http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz' failed

   status_code: 1

   status_string: unsupported protocol

   log: About to connect() to gerrit.gromacs.org port 80 (#0)

 Trying 130.237.25.133... connected

   Connected to gerrit.gromacs.org (130.237.25.133) port 80 (#0)

   GET /download/regressiontests-5.0.5.tar.gz HTTP/1.1

   Host: gerrit.gromacs.org

   Accept: */*



   HTTP/1.1 302 Found

   Date: Mon, 06 Jul 2015 09:29:46 GMT

   Server: Apache/2.2.22 (Ubuntu)

   Location:
   https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz

   Vary: Accept-Encoding

   Content-Length: 337

   Content-Type: text/html; charset=iso-8859-1

   Ignoring the response-body

   !DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN

   htmlhead

   title302 Found/title

   /headbody

   h1Found/h1

   pThe document has moved a
   href=
 https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz;
 https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz
 here/a./p


   hr

   addressApache/2.2.22 (Ubuntu) Server at gerrit.gromacs.org Port
   80/address

   /body/html

   Connection #0 to host gerrit.gromacs.org left intact

   Issue another request to this URL:
   'https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz'

   libcurl was built with SSL disabled, https: not supported!

   unsupported protocol

   Closing connection #0

 -

 what can I do?
 does installing another version of Cmake makes any difference ?



 Best Regards,
 Nima Soltani
 --
 Graduate Student of Physical Chemistry
 Department of Chemistry,
 Sharif University of Technology.
 =
 --
 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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 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.

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Re: [gmx-users] Installation problem on CRAY XC40----Gromacs-5.0.4

[Szilárd Páll]

Nothing unexpected, you can't run on the login node binaries that you
compiled for the compute nodes.
--
Szilárd


On Tue, Mar 31, 2015 at 7:48 AM, Satyabrata Das satyabrata...@gmail.com wrote:
 Thank you, I will read Cray docs again, presently trying to install with
 gcc 4.8 because
 4.9 is showing incompatibility error with the available cudatoolkit. It
 seems CPU-only
 installation is successful. However both built in test case and
 regression-test failed with the
 following error:

 [Tue Mar 31 00:44:27 2015] [c1-0c0s1n1] Fatal error in MPI_Init: Other MPI
 error, error stack:
 MPIR_Init_thread(506):
 MPID_Init(192)...: channel initialization failed
 MPID_Init(569)...:  PMI2 init failed: 1

 Kindly help,

 With best regards,

 Satyabrata Das
 --
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 * Please search the archive at 
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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[gmx-users] Installation problem on CRAY XC40----Gromacs-5.0.4

[Satyabrata Das]

Dear All,
I am trying to install Gromacs-5.0.4 on cray XC40 by using following
combinations:

(cmake-3.2.1 is compiled by myself, OS is Suse Linux X86_64)

Combination 1: INTEL 15.0/13.0 , MKL / FFTW and MPI (Cray-MPICH-7.0.5)

set FLAGS=-dynamic -O3 -funroll-loops

cmake .. -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_MPI=on
-DGMX_OPENMP=on -DGMX_GPU=off
-DCMAKE_INSTALL_PREFIX=/gromacs-5.0.4/intel-mkl-mpi -DGMX_FFT_LIBRARY=mkl
-DGMX_DOUBLE=off -DGMX_BUILD_UNITTESTS=ON -DGMX_X11=off
-DCMAKE_C_FLAGS=$FLAGS -DCMAKE_CXX_FLAGS=$FLAGS
-DCMAKE_PREFIX_PATH=/opt/cray/mpt/7.0.5/gni/mpich2-intel/140/lib:/opt/cray/mpt/7.0.5/gni/mpich2-intel/140/include:/opt/cray/mpt/7.0.5/gni/bin

It is showing the following error:

-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Could NOT find MPI_C (missing:  MPI_C_LIBRARIES MPI_C_INCLUDE_PATH)
-- Could NOT find MPI_CXX (missing:  MPI_CXX_LIBRARIES
MPI_CXX_INCLUDE_PATH)
CMake Error at cmake/gmxManageMPI.cmake:150 (message):
  MPI support requested, but no MPI compiler found.  Either set the
  C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called mpicc), or
  set the variables reported missing for MPI_C above.
Call Stack (most recent call first):
  CMakeLists.txt:464 (include)


-- Configuring incomplete, errors occurred!

Combination 2: INTEL 15.0/13.0, MKL / FFTW and MPI (Cray-MPICH-7.0.5),
CUDA(cudatoolkit/5.5.22)

It is showing the following error:
[  0%] Building NVCC (Device) object
src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_pmalloc_cuda.cu.o
In file included from
/opt/nvidia/cudatoolkit/5.5.22-1.0502.7944.3.1/include/cuda_runtime.h(59),
 from
/home/proj/14/physatya/c40/gromacs-5.0.4/src/gromacs/gmxlib/cuda_tools/
pmalloc_cuda.cu(0):
/opt/nvidia/cudatoolkit/5.5.22-1.0502.7944.3.1/include/host_config.h(72):
error: #error directive: -- unsupported ICC configuration! Only ICC 12.1 on
Linux x86_64 is supported!
  #error -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 is
supported!
   ^

CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message):
  Error generating

/home/proj/14/physatya/c40/gromacs-5.0.4/build1/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o


make[2]: ***
[src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_pmalloc_cuda.cu.o]
Error 1
make[1]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
Error 2
make: *** [all] Error 2


I have tried with GNU PrgEnv also, but unable to install. Kindly help.

With best regards,

Satyabrata Das
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Re: [gmx-users] Installation problem on CRAY XC40----Gromacs-5.0.4

[Szilárd Páll]

Hi,

You may want to read the Cray docs before attempting to compile on the
machine. You need to use the compiler wrappers (cc/CC) if you want to
run on the compute nodes and I suggest that you just use gcc 4.8/4.9
which will be both compatible with nvcc and faster.

Cheers,
--
Szilárd


On Mon, Mar 30, 2015 at 4:13 PM, Satyabrata Das satyabrata...@gmail.com wrote:
 Dear All,
 I am trying to install Gromacs-5.0.4 on cray XC40 by using following
 combinations:

 (cmake-3.2.1 is compiled by myself, OS is Suse Linux X86_64)

 Combination 1: INTEL 15.0/13.0 , MKL / FFTW and MPI (Cray-MPICH-7.0.5)

 set FLAGS=-dynamic -O3 -funroll-loops

 cmake .. -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_MPI=on
 -DGMX_OPENMP=on -DGMX_GPU=off
 -DCMAKE_INSTALL_PREFIX=/gromacs-5.0.4/intel-mkl-mpi -DGMX_FFT_LIBRARY=mkl
 -DGMX_DOUBLE=off -DGMX_BUILD_UNITTESTS=ON -DGMX_X11=off
 -DCMAKE_C_FLAGS=$FLAGS -DCMAKE_CXX_FLAGS=$FLAGS
 -DCMAKE_PREFIX_PATH=/opt/cray/mpt/7.0.5/gni/mpich2-intel/140/lib:/opt/cray/mpt/7.0.5/gni/mpich2-intel/140/include:/opt/cray/mpt/7.0.5/gni/bin

 It is showing the following error:

 -- MPI is not compatible with thread-MPI. Disabling thread-MPI.
 -- Could NOT find MPI_C (missing:  MPI_C_LIBRARIES MPI_C_INCLUDE_PATH)
 -- Could NOT find MPI_CXX (missing:  MPI_CXX_LIBRARIES
 MPI_CXX_INCLUDE_PATH)
 CMake Error at cmake/gmxManageMPI.cmake:150 (message):
   MPI support requested, but no MPI compiler found.  Either set the
   C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called mpicc), or
   set the variables reported missing for MPI_C above.
 Call Stack (most recent call first):
   CMakeLists.txt:464 (include)


 -- Configuring incomplete, errors occurred!

 Combination 2: INTEL 15.0/13.0, MKL / FFTW and MPI (Cray-MPICH-7.0.5),
 CUDA(cudatoolkit/5.5.22)

 It is showing the following error:
 [  0%] Building NVCC (Device) object
 src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_pmalloc_cuda.cu.o
 In file included from
 /opt/nvidia/cudatoolkit/5.5.22-1.0502.7944.3.1/include/cuda_runtime.h(59),
  from
 /home/proj/14/physatya/c40/gromacs-5.0.4/src/gromacs/gmxlib/cuda_tools/
 pmalloc_cuda.cu(0):
 /opt/nvidia/cudatoolkit/5.5.22-1.0502.7944.3.1/include/host_config.h(72):
 error: #error directive: -- unsupported ICC configuration! Only ICC 12.1 on
 Linux x86_64 is supported!
   #error -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 is
 supported!
^

 CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message):
   Error generating

 /home/proj/14/physatya/c40/gromacs-5.0.4/build1/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o


 make[2]: ***
 [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_pmalloc_cuda.cu.o]
 Error 1
 make[1]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
 Error 2
 make: *** [all] Error 2


 I have tried with GNU PrgEnv also, but unable to install. Kindly help.

 With best regards,

 Satyabrata Das
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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] Installation problem on CRAY XC40----Gromacs-5.0.4

[Satyabrata Das]

Thank you, I will read Cray docs again, presently trying to install with
gcc 4.8 because
4.9 is showing incompatibility error with the available cudatoolkit. It
seems CPU-only
installation is successful. However both built in test case and
regression-test failed with the
following error:

[Tue Mar 31 00:44:27 2015] [c1-0c0s1n1] Fatal error in MPI_Init: Other MPI
error, error stack:
MPIR_Init_thread(506):
MPID_Init(192)...: channel initialization failed
MPID_Init(569)...:  PMI2 init failed: 1

Kindly help,

With best regards,

Satyabrata Das
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[gmx-users] Installation problem with Gromacs 5.0.2

[PAULAMI CHATTERJEE]

Dear all

I am trying to install Gromacs 5.0.2 in a GPU machine but coming up with a 
CMake error.

Part of my error looked like this
.
Downloading: http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz
-- [download 0% complete]
CMake Error at tests/CMakeLists.txt:58 (message):
  error: downloading
  'http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz' failed
  status_code: 1
Location: https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz

  Vary: Accept-Encoding

  Content-Length: 325

  Content-Type: text/html; charset=iso-8859-1

  X-Cache: MISS from cb-proxy.boseinst.ernet.in

  X-Cache-Lookup: MISS from cb-proxy.boseinst.ernet.in:3128

  Via: 1.0 cb-proxy.boseinst.ernet.in:3128 (squid/2.6.STABLE6)

  Connection: close

  Closing connection #0

  Issue another request to this URL:
  'https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz'

  libcurl was built with SSL disabled, https: not supported!

  unsupported protocol
..

Can anyone please suggest anything to troubleshoot this?
Thanks in advance.

Paulami 
 
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Re: [gmx-users] Installation problem with Gromacs 5.0.2

[Bikash Ranjan Sahoo]

Hi,
  Don't use the  -DREGRESSIONTEST_DOWNLOAD=ON flag in cmake. if u need it
then download, configure, install and manually set the path in Cmake
configuration.

Good luck

On Wed, Dec 10, 2014 at 5:10 PM, PAULAMI CHATTERJEE 
chatterjee_paul...@yahoo.co.in wrote:

 Dear all

 I am trying to install Gromacs 5.0.2 in a GPU machine but coming up with a
 CMake error.

 Part of my error looked like this
 .
 Downloading:
 http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz
 -- [download 0% complete]
 CMake Error at tests/CMakeLists.txt:58 (message):
   error: downloading
   'http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz' failed
   status_code: 1
 Location: https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz

   Vary: Accept-Encoding

   Content-Length: 325

   Content-Type: text/html; charset=iso-8859-1

   X-Cache: MISS from cb-proxy.boseinst.ernet.in

   X-Cache-Lookup: MISS from cb-proxy.boseinst.ernet.in:3128

   Via: 1.0 cb-proxy.boseinst.ernet.in:3128 (squid/2.6.STABLE6)

   Connection: close

   Closing connection #0

   Issue another request to this URL:
   'https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz'

   libcurl was built with SSL disabled, https: not supported!

   unsupported protocol
 ..

 Can anyone please suggest anything to troubleshoot this?
 Thanks in advance.

 Paulami

 --
 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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Re: [gmx-users] Installation problem with Gromacs 5.0.2

[PAULAMI CHATTERJEE]

Hello Bikash,
Thank you for your prompt response. As you suggested  I tried to manually 
download the 'regressiontests-5.0.2.tar.gz' file from this link 
https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz But I found This 
shared file or folder link has been removed.I am sure I am missing something. 
Can you please suggest any alternative way to download the file?
Paulami
 

 On Wednesday, 10 December 2014 2:08 PM, Bikash Ranjan Sahoo 
bikash.bioinformat...@gmail.com wrote:
   

 Hi,  Don't use the  -DREGRESSIONTEST_DOWNLOAD=ON flag in cmake. if u need it 
then download, configure, install and manually set the path in Cmake 
configuration. 
Good luck
On Wed, Dec 10, 2014 at 5:10 PM, PAULAMI CHATTERJEE 
chatterjee_paul...@yahoo.co.in wrote:

Dear all

I am trying to install Gromacs 5.0.2 in a GPU machine but coming up with a 
CMake error.

Part of my error looked like this
.
Downloading: http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz
-- [download 0% complete]
CMake Error at tests/CMakeLists.txt:58 (message):
  error: downloading
  'http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz' failed
  status_code: 1
Location: https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz

  Vary: Accept-Encoding

  Content-Length: 325

  Content-Type: text/html; charset=iso-8859-1

  X-Cache: MISS from cb-proxy.boseinst.ernet.in

  X-Cache-Lookup: MISS from cb-proxy.boseinst.ernet.in:3128

  Via: 1.0 cb-proxy.boseinst.ernet.in:3128 (squid/2.6.STABLE6)

  Connection: close

  Closing connection #0

  Issue another request to this URL:
  'https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz'

  libcurl was built with SSL disabled, https: not supported!

  unsupported protocol
..

Can anyone please suggest anything to troubleshoot this?
Thanks in advance.

Paulami
 
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Re: [gmx-users] Installation problem with Gromacs 5.0.2

[Mark Abraham]

Hi,

Thanks for the report. The Box server somehow did not have the link expiry
flag set for either the 5.0.2 or 5.0.1 versions, so perhaps decided it
could change the underlying static URL, which broke the forwarding from
gerrit.gromacs.org. That's all fixed now.

Mark

On Wed, Dec 10, 2014 at 10:00 AM, PAULAMI CHATTERJEE 
chatterjee_paul...@yahoo.co.in wrote:

 Hello Bikash,
 Thank you for your prompt response. As you suggested  I tried to manually
 download the 'regressiontests-5.0.2.tar.gz' file from this link
 https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz But I found
 This shared file or folder link has been removed.I am sure I am missing
 something. Can you please suggest any alternative way to download the file?
 Paulami


  On Wednesday, 10 December 2014 2:08 PM, Bikash Ranjan Sahoo 
 bikash.bioinformat...@gmail.com wrote:


  Hi,  Don't use the  -DREGRESSIONTEST_DOWNLOAD=ON flag in cmake. if u
 need it then download, configure, install and manually set the path in
 Cmake configuration.
 Good luck
 On Wed, Dec 10, 2014 at 5:10 PM, PAULAMI CHATTERJEE 
 chatterjee_paul...@yahoo.co.in wrote:

 Dear all

 I am trying to install Gromacs 5.0.2 in a GPU machine but coming up with a
 CMake error.

 Part of my error looked like this
 .
 Downloading:
 http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz
 -- [download 0% complete]
 CMake Error at tests/CMakeLists.txt:58 (message):
   error: downloading
   'http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz' failed
   status_code: 1
 Location: https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz

   Vary: Accept-Encoding

   Content-Length: 325

   Content-Type: text/html; charset=iso-8859-1

   X-Cache: MISS from cb-proxy.boseinst.ernet.in

   X-Cache-Lookup: MISS from cb-proxy.boseinst.ernet.in:3128

   Via: 1.0 cb-proxy.boseinst.ernet.in:3128 (squid/2.6.STABLE6)

   Connection: close

   Closing connection #0

   Issue another request to this URL:
   'https://kth.box.com/shared/static/oymh61gk1ya9qoden2tn.gz'

   libcurl was built with SSL disabled, https: not supported!

   unsupported protocol
 ..

 Can anyone please suggest anything to troubleshoot this?
 Thanks in advance.

 Paulami

 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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 send a mail to gmx-users-requ...@gromacs.org.





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[gmx-users] Installation: problem with Mkl library

[lucaam86]

Hi
I'm desperately trying to install gromacs on Win7. I'm not very experienced.
I proceeded to install with CMake but at some point I keep giving this
error:
/
CMake Error at CMakeLists.txt:969 (message):
  Linking with MKL was requested, but was not successful.  The include path
  to mkl.h in MKL_INCLUDE_DIR, and the link libraries in
  MKL_LIBRARIES=C:/Program
 
Files/Intel/MKL/10.2.2.025/ia64/lib/mkl_solver_ilp64_sequential.lib,C:/Program
  Files/Intel/MKL/10.2.2.025/ia64/lib/mkl_intel_lp64.lib,C:/Program
  Files/Intel/MKL/10.2.2.025/ia64/lib/mkl_sequential.lib,C:/Program
  Files/Intel/MKL/10.2.2.025/ia64/lib/mkl_core.lib need to match what the
MKL
  documentation says you need for your system.  Use full paths to library
  files, in the right order, and separated by semicolons./


There attach a screenshot of how I set CMake:
https://www.dropbox.com/s/cd0rsgynjqfcp40/Screenshot%202014-01-30%2015.13.31.png

Could you help me figure out where am I wrong?
Thank you
Luca



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