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Subject:

Issues compiling and running tests

From:

Mark Egan-Fuller <[log in to unmask]>

Reply-To:

DL_POLY Mailing List <[log in to unmask]>

Date:

Wed, 29 Nov 2017 12:50:23 +0000

Content-Type:

multipart/mixed

Parts/Attachments:
Parts/Attachments

text/plain (137 lines) , cluster_cmake.out (1 lines) , cluster_LastTest.log (4640 lines) , cluster_make.out (1 lines) , cluster_make_test.out (1 lines) , local_cmake.out (1 lines) , local_LastTest.log (4496 lines) , local_make.out (1 lines) , local_make_test.out (1 lines) 

We've been having issues attempting to compile DL_POLY via cmake, despite
repeated attempts on multiple machines running different versions.

Below I've listed the steps we use and details of the machines,
I've attached the full output and LastTest.log to this email.

## Steps On HPC Cluster

Using:

* Centos 7
* openmpi 2.1.0
* python 3.6.3
* cmake 3.8.0
* gfortran 4.8.5

We use environment modules on the cluster for openmpi, python and cmake.

Steps:

```
tar -xzvf dl_poly_4.08.tar.gz
cd dl_poly_4.08
mkdir cluster_build
cd cluster_build

FFLAGS="-O3 -mtune=native" cmake -DBUILD_SHARED_LIBS=ON \
                                  -DBUILD_TESTING=ON \
                                  -DMPI_NPROCS=32 \
                                  -DPYTHON_EXECUTABLE=/share/apps/centos7/python/3.6.3/bin/python \
                                  ..

make -j 32

make test
```

## Steps On Local Machine

Using:

* Arch Linux
* openmpi 2.1.1
* python 3.6.3
* cmake 3.9.6
* gfortran 7.2.0

Steps:

```
tar -xzvf dl_poly_4.08.tar.gz
cd dl_poly_4.08
mkdir local_build
cd local_build

FFLAGS="-O3 -mtune=native" cmake -DBUILD_SHARED_LIBS=ON \
                                  -DBUILD_TESTING=ON \
                                  -DMPI_NPROCS=4 \
                                  ..

make -j 4

make test
```

## Tests On HPC Cluster:

```
60% tests passed, 10 tests failed out of 25

Total Test time (real) = 253.44 sec

The following tests FAILED:
	  1 - TEST01 (Failed)
	  3 - TEST03 (Failed)
	  4 - TEST04 (Failed)
	  8 - TEST08 (Failed)
	  9 - TEST09 (Failed)
	 18 - TEST18 (Failed)
	 19 - TEST19 (Failed)
	 20 - TEST20 (Failed)
	 21 - TEST21 (Failed)
	 22 - TEST22 (Failed)
Errors while running CTest
make: *** [test] Error 8
```

## Tests On Local machine:

```
76% tests passed, 6 tests failed out of 25

Total Test time (real) = 191.48 sec

The following tests FAILED:
	  7 - TEST07 (Failed)
	  8 - TEST08 (Failed)
	  9 - TEST09 (Failed)
	 20 - TEST20 (Failed)
	 21 - TEST21 (Failed)
	 22 - TEST22 (Failed)
Errors while running CTest
make: *** [Makefile:73: test] Error 8
```

We also see:

```
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
```

This may be the source of the issue but I'm not sure as it only appears on the
local build.


Any guidance on this appreciated, I'm expecting it to be something I've done
wrong somewhere, a missing or incorrect option, etc.


Regards,


-- 
Mark Egan-Fuller
Research Applications Team Leader
ITS Research

Support Email: [log in to unmask]
Documentation: https://docs.hpc.qmul.ac.uk/

########################################################################

To unsubscribe from the DLPOLY list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=DLPOLY&A=1




-- Found MPI_Fortran: /share/apps/centos7/openmpi/2.1.0/lib/libmpi_usempi.so;/share/apps/centos7/openmpi/2.1.0/lib/libmpi_mpifh.so;/share/apps/centos7/openmpi/2.1.0/lib/libmpi.so  
-- MPI_Fortran_INCLUDE_PATH /share/apps/centos7/openmpi/2.1.0/include;/share/apps/centos7/openmpi/2.1.0/lib
-- Build with MPI support!
-- default value for builder will be used
-- building on ccn2.apocrita
-- Build without OPENMP support
-- Build for CPU host
-- Build without netcdf support
-- Build without KIM support
-- Build without PLUMED support
-- Build without extra timing support
-- Build without code coverage testing
-- Build without forcheck support!
-- Build with testing support support: make test
-- Found PythonInterp: /share/apps/centos7/python/3.6.3/bin/python (found suitable version "3.6.3", minimum required is "3.0") 
-- Trying to download TEST01.tar.gz
-- Trying to download TEST02.tar.gz
-- Trying to download TEST03.tar.gz
-- Trying to download TEST04.tar.gz
-- Trying to download TEST05.tar.gz
-- Trying to download TEST06.tar.gz
-- Trying to download TEST07.tar.gz
-- Trying to download TEST08.tar.gz
-- Trying to download TEST09.tar.gz
-- Trying to download TEST10.tar.gz
-- Trying to download TEST11.tar.gz
-- Trying to download TEST12.tar.gz
-- Trying to download TEST13.tar.gz
-- Trying to download TEST14.tar.gz
-- Trying to download TEST15.tar.gz
-- Trying to download TEST16.tar.gz
-- Trying to download TEST17.tar.gz
-- Trying to download TEST18.tar.gz
-- Trying to download TEST19.tar.gz
-- Trying to download TEST20.tar.gz
-- Trying to download TEST21.tar.gz
-- Trying to download TEST22.tar.gz
-- Trying to download TEST23.tar.gz
-- Trying to download TEST24.tar.gz
-- Trying to download TEST25.tar.gz
-- Configuring done
-- Generating done
-- Build files have been written to: /data/home/aaw702/compile/dl_poly_4.08/cluster_build




########################################################################



To unsubscribe from the DLPOLY list, click the following link:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=DLPOLY&A=1




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[100%] Linking Fortran shared library ../lib64/libdlpoly.so
[100%] Built target dlpoly
Scanning dependencies of target DLPOLY.Z
[100%] Building Fortran object source/CMakeFiles/DLPOLY.Z.dir/dl_poly.f90.o
[100%] Linking Fortran executable ../bin/DLPOLY.Z
[100%] Built target DLPOLY.Z




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Running tests...
Test project /data/home/aaw702/compile/dl_poly_4.08/cluster_build
      Start  1: TEST01
 1/25 Test  #1: TEST01 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
] 12.16 sec
      Start  2: TEST02
 2/25 Test  #2: TEST02 ...........................   Passed   12.37 sec
      Start  3: TEST03
 3/25 Test  #3: TEST03 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
] 15.13 sec
      Start  4: TEST04
 4/25 Test  #4: TEST04 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
] 13.72 sec
      Start  5: TEST05
 5/25 Test  #5: TEST05 ...........................   Passed    9.73 sec
      Start  6: TEST06
 6/25 Test  #6: TEST06 ...........................   Passed    7.83 sec
      Start  7: TEST07
 7/25 Test  #7: TEST07 ...........................   Passed   13.71 sec
      Start  8: TEST08
 8/25 Test  #8: TEST08 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
]  7.64 sec
      Start  9: TEST09
 9/25 Test  #9: TEST09 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
] 13.85 sec
      Start 10: TEST10
10/25 Test #10: TEST10 ...........................   Passed   11.29 sec
      Start 11: TEST11
11/25 Test #11: TEST11 ...........................   Passed    7.48 sec
      Start 12: TEST12
12/25 Test #12: TEST12 ...........................   Passed    7.39 sec
      Start 13: TEST13
13/25 Test #13: TEST13 ...........................   Passed    7.30 sec
      Start 14: TEST14
14/25 Test #14: TEST14 ...........................   Passed    6.94 sec
      Start 15: TEST15
15/25 Test #15: TEST15 ...........................   Passed    7.33 sec
      Start 16: TEST16
16/25 Test #16: TEST16 ...........................   Passed    7.09 sec
      Start 17: TEST17
17/25 Test #17: TEST17 ...........................   Passed    7.36 sec
      Start 18: TEST18
18/25 Test #18: TEST18 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
] 15.49 sec
      Start 19: TEST19
19/25 Test #19: TEST19 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
]  8.73 sec
      Start 20: TEST20
20/25 Test #20: TEST20 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
] 11.57 sec
      Start 21: TEST21
21/25 Test #21: TEST21 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
] 14.29 sec
      Start 22: TEST22
22/25 Test #22: TEST22 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
]  9.02 sec
      Start 23: TEST23
23/25 Test #23: TEST23 ...........................   Passed    7.62 sec
      Start 24: TEST24
24/25 Test #24: TEST24 ...........................   Passed   10.06 sec
      Start 25: TEST25
25/25 Test #25: TEST25 ...........................   Passed    8.08 sec

60% tests passed, 10 tests failed out of 25

Total Test time (real) = 253.44 sec

The following tests FAILED:
	  1 - TEST01 (Failed)
	  3 - TEST03 (Failed)
	  4 - TEST04 (Failed)
	  8 - TEST08 (Failed)
	  9 - TEST09 (Failed)
	 18 - TEST18 (Failed)
	 19 - TEST19 (Failed)
	 20 - TEST20 (Failed)
	 21 - TEST21 (Failed)
	 22 - TEST22 (Failed)
Errors while running CTest
make: *** [test] Error 8




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-- The Fortran compiler identification is GNU 7.2.0
-- Check for working Fortran compiler: /usr/bin/f95
-- Check for working Fortran compiler: /usr/bin/f95  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/f95 supports Fortran 90
-- Checking whether /usr/bin/f95 supports Fortran 90 -- yes
-- Found MPI_Fortran: /usr/lib/openmpi/libmpi_usempif08.so;/usr/lib/openmpi/libmpi_usempi_ignore_tkr.so;/usr/lib/openmpi/libmpi_mpifh.so;/usr/lib/openmpi/libmpi.so  
-- MPI_Fortran_INCLUDE_PATH /usr/include;/usr/lib/openmpi
-- Build with MPI support!
-- default value for builder will be used
-- building on cogitator-ext
-- Build without OPENMP support
-- Build for CPU host
-- Build without netcdf support
-- Build without KIM support
-- Build without PLUMED support
-- Build without extra timing support
-- Build without code coverage testing
-- Build without forcheck support!
-- Build with testing support support: make test
-- Found PythonInterp: /usr/bin/python3 (found suitable version "3.6.3", minimum required is "3.0") 
-- Trying to download TEST01.tar.gz
-- Trying to download TEST02.tar.gz
-- Trying to download TEST03.tar.gz
-- Trying to download TEST04.tar.gz
-- Trying to download TEST05.tar.gz
-- Trying to download TEST06.tar.gz
-- Trying to download TEST07.tar.gz
-- Trying to download TEST08.tar.gz
-- Trying to download TEST09.tar.gz
-- Trying to download TEST10.tar.gz
-- Trying to download TEST11.tar.gz
-- Trying to download TEST12.tar.gz
-- Trying to download TEST13.tar.gz
-- Trying to download TEST14.tar.gz
-- Trying to download TEST15.tar.gz
-- Trying to download TEST16.tar.gz
-- Trying to download TEST17.tar.gz
-- Trying to download TEST18.tar.gz
-- Trying to download TEST19.tar.gz
-- Trying to download TEST20.tar.gz
-- Trying to download TEST21.tar.gz
-- Trying to download TEST22.tar.gz
-- Trying to download TEST23.tar.gz
-- Trying to download TEST24.tar.gz
-- Trying to download TEST25.tar.gz
-- Configuring done
-- Generating done
-- Build files have been written to: /home/markeganfuller/scratchpads/9538_dl_poly/dl_poly_4.08/local_build




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Scanning dependencies of target dlpolycore
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Running tests...
Test project /home/markeganfuller/scratchpads/9538_dl_poly/dl_poly_4.08/local_build
      Start  1: TEST01
 1/25 Test  #1: TEST01 ...........................   Passed    4.83 sec
      Start  2: TEST02
 2/25 Test  #2: TEST02 ...........................   Passed   13.60 sec
      Start  3: TEST03
 3/25 Test  #3: TEST03 ...........................   Passed   24.97 sec
      Start  4: TEST04
 4/25 Test  #4: TEST04 ...........................   Passed   16.94 sec
      Start  5: TEST05
 5/25 Test  #5: TEST05 ...........................   Passed    8.52 sec
      Start  6: TEST06
 6/25 Test  #6: TEST06 ...........................   Passed    4.82 sec
      Start  7: TEST07
 7/25 Test  #7: TEST07 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
] 14.41 sec
      Start  8: TEST08
 8/25 Test  #8: TEST08 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
]  2.93 sec
      Start  9: TEST09
 9/25 Test  #9: TEST09 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
]  9.08 sec
      Start 10: TEST10
10/25 Test #10: TEST10 ...........................   Passed    7.09 sec
      Start 11: TEST11
11/25 Test #11: TEST11 ...........................   Passed    4.75 sec
      Start 12: TEST12
12/25 Test #12: TEST12 ...........................   Passed    3.16 sec
      Start 13: TEST13
13/25 Test #13: TEST13 ...........................   Passed    3.36 sec
      Start 14: TEST14
14/25 Test #14: TEST14 ...........................   Passed    3.45 sec
      Start 15: TEST15
15/25 Test #15: TEST15 ...........................   Passed    3.57 sec
      Start 16: TEST16
16/25 Test #16: TEST16 ...........................   Passed    3.28 sec
      Start 17: TEST17
17/25 Test #17: TEST17 ...........................   Passed    3.83 sec
      Start 18: TEST18
18/25 Test #18: TEST18 ...........................   Passed   14.32 sec
      Start 19: TEST19
19/25 Test #19: TEST19 ...........................   Passed    5.55 sec
      Start 20: TEST20
20/25 Test #20: TEST20 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
]  7.46 sec
      Start 21: TEST21
21/25 Test #21: TEST21 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
] 11.35 sec
      Start 22: TEST22
22/25 Test #22: TEST22 ...........................***Failed  Required regular expression not found.Regex=[Status: PASSED
]  5.67 sec
      Start 23: TEST23
23/25 Test #23: TEST23 ...........................   Passed    5.09 sec
      Start 24: TEST24
24/25 Test #24: TEST24 ...........................   Passed    4.35 sec
      Start 25: TEST25
25/25 Test #25: TEST25 ...........................   Passed    5.12 sec

76% tests passed, 6 tests failed out of 25

Total Test time (real) = 191.48 sec

The following tests FAILED:
	  7 - TEST07 (Failed)
	  8 - TEST08 (Failed)
	  9 - TEST09 (Failed)
	 20 - TEST20 (Failed)
	 21 - TEST21 (Failed)
	 22 - TEST22 (Failed)
Errors while running CTest
make: *** [Makefile:73: test] Error 8




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