[saravana]

I have this error, could solve me what is going on.

./test.py “mpirun -np 8 ../../genesis-1.4.0/bin/spdyn”
=======================================================================
Regression tests for MD
=======================================================================
———————————————————————–
Running ./test_common/cryoEM/All_atom/…
$ mpirun -np 8 /home/msti/Descargas/japan/genesis-1.4.0/bin/spdyn inp 1> test 2> error

Checking ./test_common/cryoEM/All_atom
Checking diff between ref and test…

Failure at step 1 (tolerance = 1.00e-08(ene), 1.00e-06(virial))
Step 1
VOLUME EMCORR VDWAALS ANGLE RMSGRESTRAINT_TOTAL UREY-BRADLEY POTENTIAL_ENE DIHEDRAL IMPROPER STEP CMAP TEMPERATURE TIME ELECT BOND TOTAL_ENE KINETIC_ENE
< 88560.0000 0.9808 3870.0665 165.2156 13.7426 19.2068 16.7186 -33287.1870 271.8235 6.7731 1 -80.3685 146.2186 0.0020 -37613.0277 56.4052 -30486.4387 2800.7483
> TEMPERATURE ELECT CMAP ANGLE RMSG EMCORR UREY POTENTIAL_ENE -BRADLEY DIHEDRAL STEP IMPROPERRESTRAINT_TOTAL TIME VDWAALS BOND TOTAL_ENE KINETIC_ENE

Step 2
VOLUME EMCORR VDWAALS ANGLE RMSGRESTRAINT_TOTAL UREY-BRADLEY POTENTIAL_ENE DIHEDRAL IMPROPER STEP CMAP TEMPERATURE TIME ELECT BOND TOTAL_ENE KINETIC_ENE
< 88560.0000 0.9808 3892.9107 212.3635 13.9190 19.2186 23.7504 -33031.3778 277.6361 8.9754 2 -79.4943 133.2759 0.0040 -37466.0607 79.3224 -30478.5394 2552.8384
> 88560.0000 0.9808 3861.7187 146.1458 13.6621 19.1964 13.8892 -33387.4257 269.1582 5.9646 0 -81.1417 151.2769 0.0000 -37666.7878 44.4311 -30489.7867 2897.6390

Step 3
VOLUME EMCORR VDWAALS ANGLE RMSGRESTRAINT_TOTAL UREY-BRADLEY POTENTIAL_ENE DIHEDRAL IMPROPER STEP CMAP TEMPERATURE TIME ELECT BOND TOTAL_ENE KINETIC_ENE
< 88560.0000 0.9808 3926.1604 243.8901 13.9986 19.2319 29.4911 -32736.3126 284.0317 11.4604 3 -78.6223 118.2048 0.0060 -37265.1648 93.2087 -30472.1551 2264.1576
> TEMPERATURE ELECT CMAP ANGLE RMSG EMCORR UREY POTENTIAL_ENE -BRADLEY DIHEDRAL STEP IMPROPERRESTRAINT_TOTAL TIME VDWAALS BOND TOTAL_ENE KINETIC_ENE

———————————————————————–
Running ./test_common/cryoEM/Go_model/…
$ mpirun -np 8 /home/msti/Descargas/japan/genesis-1.4.0/bin/spdyn inp 1> test 2> error

Aborted…

———————————————————————–
Running ./test_common/dna/CUTOFF/…
$ mpirun -np 8 /home/msti/Descargas/japan/genesis-1.4.0/bin/spdyn inp 1> test 2> error

Checking ./test_common/dna/CUTOFF
Checking diff between ref and test…

Failure at step 4 (tolerance = 1.00e-08(ene), 1.00e-06(virial))
Step 4
ANGLE VOLUME PRESSXX BOXY BOXX BOXZ VIRIAL PRESSZZ TEMPERATURE RMSG BOND DIHEDRAL UREY-BRADLEY POTENTIAL_ENE PRESSURE PRESSYY TOTAL_ENE KINETIC_ENE IMPROPER ELECT STEP VDWAALS TIME
< 173.7119 262144.0000 -4255.0240 64.0000 64.0000 64.0000 -16582.4836 -4122.2434 27.2479 15.8431 68.8180 619.6358 111.5704 -102496.1755 -4108.3746 -3947.8563 -101182.6016 1313.5739 3.7138 -116319.3102 4 12845.6848 0.0040
> ANGLE TEMPERATURE PRESSURE BOXX VOLUME BOXY BOXZ PRESSYY ELECT RMSG BOND -BRADLEY UREY POTENTIAL_ENE VIRIAL PRESSXX TOTAL_ENE KINETIC_ENE DIHEDRAL VDWAALS STEP IMPROPER TIME

Step 6
ANGLE VOLUME PRESSXX BOXY BOXX BOXZ VIRIAL PRESSZZ TEMPERATURE RMSG BOND DIHEDRAL UREY-BRADLEY POTENTIAL_ENE PRESSURE PRESSYY TOTAL_ENE KINETIC_ENE IMPROPER ELECT STEP VDWAALS TIME
< 174.2318 262144.0000 -4275.8942 64.0000 64.0000 64.0000 -16608.4299 -4129.5127 27.1825 15.8320 67.1799 618.8990 111.4559 -102493.2047 -4115.7107 -3941.7253 -101182.7818 1310.4229 3.5963 -116283.6046 6 12815.0368 0.0060
> 171.9593 262144.0000 -4237.2973 64.0000 64.0000 64.0000 -16582.0248 -4112.2051 28.0024 15.8565 70.0352 620.2854 111.8679 -102532.5392 -4101.9122 -3956.2341 -101182.5937 1349.9455 3.8520 -116398.6625 2 12888.1235 0.0020

Step 8
ANGLE VOLUME PRESSXX BOXY BOXX BOXZ VIRIAL PRESSZZ TEMPERATURE RMSG BOND DIHEDRAL UREY-BRADLEY POTENTIAL_ENE PRESSURE PRESSYY TOTAL_ENE KINETIC_ENE IMPROPER ELECT STEP VDWAALS TIME
< 175.0115 262144.0000 -4295.9745 64.0000 64.0000 64.0000 -16641.4934 -4132.4057 27.5852 15.8256 65.5665 618.2434 111.5587 -102512.8028 -4120.9739 -3934.5414 -101182.9670 1329.8359 3.5664 -116284.0159 8 12797.2667 0.0080
> ANGLE TEMPERATURE PRESSURE BOXX VOLUME BOXY BOXZ PRESSYY ELECT RMSG BOND -BRADLEY UREY POTENTIAL_ENE VIRIAL PRESSXX TOTAL_ENE KINETIC_ENE DIHEDRAL VDWAALS STEP IMPROPER TIME

———————————————————————–
Running ./test_common/dna/PME/…
$ mpirun -np 8 /home/msti/Descargas/japan/genesis-1.4.0/bin/spdyn inp 1> test 2> error
Traceback (most recent call last):
File “./test.py”, line 220, in <module>
test.read(testname)
File “/home/msti/Descargas/japan/tests-1.5.0/regression_test/genesis.py”, line 41, in read
self.parse(text_list)
File “/home/msti/Descargas/japan/tests-1.5.0/regression_test/genesis.py”, line 107, in parse
self.dict_append(title, text, data)
File “/home/msti/Descargas/japan/tests-1.5.0/regression_test/genesis.py”, line 117, in dict_append
self.dict_text[title] = self.dict_text[title] + text_transpose
IndexError: list index out of range
msti@msti-HP-Notebook:~/Descargas/japan/tests-1.5.0/regression_test$

 

 

 

 

[saravana]

Hi anyone can solve my issue?

[tmori]

Dear Saravana,

First of all, please see the User manual ver. 1.4.0 page 18. You can find some hints to solve the issues.

1) We are providing about 50 test sets. How many errors did you encounter?

2) Could you let us know your computational environment (laptop or workstation, OS, memory size, compiler, and etc) ? Then, we may be able to suggest possible solutions.

Bests,

Takaharu Mori