Re: [gmx-users] Gromacs Install problem

2020-03-14 Thread Paul bauer

Hello,

if you have found a bug in the multi-dimensional array please report it 
on redmine.gromacs.org so we can fix it, together with the build 
configuration that causes it.


Cheers

Paul

On 14/03/2020 00:51, Alexander Tzanov wrote:

The new version from March 2020.1 is buggy. Try version 2020. There is another 
bug in multidimensional array ...

Alex

On Mar 13, 2020 1:54 PM, xuan Zhang  wrote:
Hi,

When I install the Gromacs on Linux, the cmake occurs error like below. I
am a newer on this software. I appreciate very much that you can help me.

Best regards,
Xuan

**/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON
CMake Error at cmake/FindLibStdCpp.cmake:162 (message):
   GROMACS requires C++14, but a test of such functionality in the C++
   standard library failed to compile.  The g++ found at /usr/bin/g++ had a
   suitable version, so ;something else must be the problem
Call Stack (most recent call first):
   CMakeLists.txt:69 (find_package)


-- Configuring incomplete, errors occurred!
See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log".
See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log".


*#cmakeerror.log as below:*

Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following
output:
Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f
CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build
make[1]: Entering directory
'/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o
/sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++
   -gcc-name=/usr/bin/g++ -DCXX14_COMPILES   -std=c++14 -o
CMakeFiles/cmTC_203a2.dir/src.cxx.o -c
/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx
/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error:
namespace "std" has no member "cbegin"
   int main() { int a[2]; std::cbegin(a); }
   ^

compilation aborted for
/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2)
CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target
'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed
make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2
make[1]: Leaving directory
'/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp'
Makefile:138: recipe for target 'cmTC_203a2/fast' failed
make: *** [cmTC_203a2/fast] Error 2


Source file was:
#include 
int main() { int a[2]; std::cbegin(a); }

--
*Xuan Zhang*

PhD  Candidate
China University of Petroleum(East China)
School of Petroleum Engineering
No.66 Changjiang West Road, Qingdao


Visiting scholar (2017.12-2018.12)
The University of Texas at Austin
Cockrell School of Engineering
McKetta Department of Chemical Engineering
200 E Dean Keeton St. Stop C0400
CPE 5.428

*(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7...@gmail.com
--
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--
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594

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Re: [gmx-users] Gromacs Install problem

2020-03-13 Thread Alexander Tzanov
The new version from March 2020.1 is buggy. Try version 2020. There is another 
bug in multidimensional array ...

Alex

On Mar 13, 2020 1:54 PM, xuan Zhang  wrote:
Hi,

When I install the Gromacs on Linux, the cmake occurs error like below. I
am a newer on this software. I appreciate very much that you can help me.

Best regards,
Xuan

**/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON
CMake Error at cmake/FindLibStdCpp.cmake:162 (message):
  GROMACS requires C++14, but a test of such functionality in the C++
  standard library failed to compile.  The g++ found at /usr/bin/g++ had a
  suitable version, so ;something else must be the problem
Call Stack (most recent call first):
  CMakeLists.txt:69 (find_package)


-- Configuring incomplete, errors occurred!
See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log".
See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log".


*#cmakeerror.log as below:*

Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following
output:
Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f
CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build
make[1]: Entering directory
'/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o
/sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++
  -gcc-name=/usr/bin/g++ -DCXX14_COMPILES   -std=c++14 -o
CMakeFiles/cmTC_203a2.dir/src.cxx.o -c
/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx
/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error:
namespace "std" has no member "cbegin"
  int main() { int a[2]; std::cbegin(a); }
  ^

compilation aborted for
/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2)
CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target
'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed
make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2
make[1]: Leaving directory
'/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp'
Makefile:138: recipe for target 'cmTC_203a2/fast' failed
make: *** [cmTC_203a2/fast] Error 2


Source file was:
#include 
int main() { int a[2]; std::cbegin(a); }

--
*Xuan Zhang*

PhD  Candidate
China University of Petroleum(East China)
School of Petroleum Engineering
No.66 Changjiang West Road, Qingdao


Visiting scholar (2017.12-2018.12)
The University of Texas at Austin
Cockrell School of Engineering
McKetta Department of Chemical Engineering
200 E Dean Keeton St. Stop C0400
CPE 5.428

*(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7...@gmail.com
--
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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Re: [gmx-users] Gromacs Install problem

2020-03-13 Thread Alexander Tzanov
For that error you may use normal and better Intel compiler or gcc above 6.3.

The 2020.1 compiles well after correcting stupid bug in multidimensional array 
routine and with use of Intel 19 and gcc above 6. I use 7.3

Your compiler is too old to support C++14 but there other problem as well

Alex




On Mar 13, 2020 1:54 PM, xuan Zhang  wrote:
Hi,

When I install the Gromacs on Linux, the cmake occurs error like below. I
am a newer on this software. I appreciate very much that you can help me.

Best regards,
Xuan

**/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON
CMake Error at cmake/FindLibStdCpp.cmake:162 (message):
  GROMACS requires C++14, but a test of such functionality in the C++
  standard library failed to compile.  The g++ found at /usr/bin/g++ had a
  suitable version, so ;something else must be the problem
Call Stack (most recent call first):
  CMakeLists.txt:69 (find_package)


-- Configuring incomplete, errors occurred!
See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log".
See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log".


*#cmakeerror.log as below:*

Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following
output:
Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f
CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build
make[1]: Entering directory
'/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o
/sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++
  -gcc-name=/usr/bin/g++ -DCXX14_COMPILES   -std=c++14 -o
CMakeFiles/cmTC_203a2.dir/src.cxx.o -c
/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx
/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error:
namespace "std" has no member "cbegin"
  int main() { int a[2]; std::cbegin(a); }
  ^

compilation aborted for
/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2)
CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target
'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed
make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2
make[1]: Leaving directory
'/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp'
Makefile:138: recipe for target 'cmTC_203a2/fast' failed
make: *** [cmTC_203a2/fast] Error 2


Source file was:
#include 
int main() { int a[2]; std::cbegin(a); }

--
*Xuan Zhang*

PhD  Candidate
China University of Petroleum(East China)
School of Petroleum Engineering
No.66 Changjiang West Road, Qingdao


Visiting scholar (2017.12-2018.12)
The University of Texas at Austin
Cockrell School of Engineering
McKetta Department of Chemical Engineering
200 E Dean Keeton St. Stop C0400
CPE 5.428

*(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7...@gmail.com
--
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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mail to gmx-users-requ...@gromacs.org.


Re: [gmx-users] Gromacs Install problem

2020-03-13 Thread xuan Zhang
Hi,

For now, I have added the compiler to cmake and it works. But in the
*make *step,
the errors were shown as below. Thank you very much.

Best regards,
Xuan

src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make:79: recipe for target
'src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o'
failed
make[2]: ***
[src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o]
Error 1
CMakeFiles/Makefile2:4229: recipe for target
'src/gromacs/CMakeFiles/lmfit_objlib.dir/all' failed
make[1]: *** [src/gromacs/CMakeFiles/lmfit_objlib.dir/all] Error 2
Makefile:179: recipe for target 'all' failed
make: *** [all] Error 2
liy0i@kw60520:/data16/XUAN/gromacs-2020.1/build$ ./configure
-bash: ./configure: No such file or directory



On Sat, Mar 14, 2020 at 1:53 AM xuan Zhang  wrote:

> Hi,
>
> When I install the Gromacs on Linux, the cmake occurs error like below. I
> am a newer on this software. I appreciate very much that you can help me.
>
> Best regards,
> Xuan
>
> **/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ON
> CMake Error at cmake/FindLibStdCpp.cmake:162 (message):
>   GROMACS requires C++14, but a test of such functionality in the C++
>   standard library failed to compile.  The g++ found at /usr/bin/g++ had a
>   suitable version, so ;something else must be the problem
> Call Stack (most recent call first):
>   CMakeLists.txt:69 (find_package)
>
>
> -- Configuring incomplete, errors occurred!
> See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log".
> See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log".
>
>
> *#cmakeerror.log as below:*
>
> Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following
> output:
> Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp
>
> Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f
> CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build
> make[1]: Entering directory
> '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp'
> Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o
> /sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++
>   -gcc-name=/usr/bin/g++ -DCXX14_COMPILES   -std=c++14 -o
> CMakeFiles/cmTC_203a2.dir/src.cxx.o -c
> /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx
> /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error:
> namespace "std" has no member "cbegin"
>   int main() { int a[2]; std::cbegin(a); }
>   ^
>
> compilation aborted for
> /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2)
> CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target
> 'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed
> make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2
> make[1]: Leaving directory
> '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp'
> Makefile:138: recipe for target 'cmTC_203a2/fast' failed
> make: *** [cmTC_203a2/fast] Error 2
>
>
> Source file was:
> #include 
> int main() { int a[2]; std::cbegin(a); }
>
> --
> *Xuan Zhang*
>
> PhD  Candidate
> China University of Petroleum(East China)
> School of Petroleum Engineering
> No.66 Changjiang West Road, Qingdao
>
>
> Visiting scholar (2017.12-2018.12)
> The University of Texas at Austin
> Cockrell School of Engineering
> McKetta Department of Chemical Engineering
> 200 E Dean Keeton St. Stop C0400
> CPE 5.428
>
> *(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7...@gmail.com
>


-- 
*Xuan Zhang*

PhD  Candidate
China University of Petroleum(East China)
School of Petroleum Engineering
No.66 Changjiang West Road, Qingdao


Visiting scholar (2017.12-2018.12)
The University of Texas at Austin
Cockrell School of Engineering
McKetta Department of Chemical Engineering
200 E Dean Keeton St. Stop C0400
CPE 5.428

*(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7...@gmail.com
-- 
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.