[AMBER] 转发: Amber20 install problem (Geng Dong)

From: 东庚 <gdong.stu.edu.cn>
Date: Wed, 19 Aug 2020 01:25:04 +0000

Hi all,
We have problems when we install the amber20. What we did are shown as following
tar xvf Amber20.tar.bz2
tar xvf AmberTools20.tar.bz2
cd amber20_src/build
./run_cmake
make install

source /xxxxx/amber2020/amber20/amber.sh

cd $AMBERHOME
make test.serial

However, we failed in make test.serial. We got these
1474 file comparisons passed
30 file comparisons failed (3 of which can be ignored)
594 tests experienced errors
Test log file saved as /home/Kai/software/amber20///logs/test_at_serial/2020-07-21_11-42-49.log
Test diffs file saved as /home/Kai/software/amber20///logs/test_at_serial/2020-07-21_11-42-49.diff

Some of the errors are shown here

cd 2048_wat_gem && ./Run.2048_wat_nvt_gem.pmemd.gem
At line 104 of file /home/Kai/software/amber20_src/AmberTools/src/gem.pmemd/src/nextinpcrd_section.F90
Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:
#0 0x7f88965c6eea
#1 0x7f88965c7a45
#2 0x7f88965c81fc
#3 0x7f88966926ae
#4 0x7f88966957f4
#5 0x561a4309f4e9
#6 0x561a43024f25
#7 0x561a4308cebc
#8 0x561a430b9e95
#9 0x561a42fc866e
#10 0x7f8895fc3b96
#11 0x561a42fc86a9
#12 0xffffffffffffffff
  ./Run.2048_wat_nvt_gem.pmemd.gem: Program error
Makefile:1607: recipe for target 'test.gem.pmemd.yes' failed
make[2]: [test.gem.pmemd.yes] Error 1 (已忽略)
cd 2048_wat_gem && ./Run.2048_wat_MCbar_gem.pmemd.gem
At line 104 of file /home/Kai/software/amber20_src/AmberTools/src/gem.pmemd/src/nextinpcrd_section.F90
Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:
#0 0x7f371f68deea
#1 0x7f371f68ea45
#2 0x7f371f68f1fc
#3 0x7f371f7596ae
#4 0x7f371f75c7f4
#5 0x55f3aa1604e9
#6 0x55f3aa0e5f25
#7 0x55f3aa14debc
#8 0x55f3aa17ae95
#9 0x55f3aa08966e
#10 0x7f371f08ab96
#11 0x55f3aa0896a9
#12 0xffffffffffffffff
  ./Run.2048_wat_MCbar_gem.pmemd.gem: Program error
Makefile:1607: recipe for target 'test.gem.pmemd.yes' failed
make[2]: [test.gem.pmemd.yes] Error 1 (已忽略)
cd amoeba_formbox && ./Run.amoeba_formbox.pmemd.gem
At line 174 of file /home/Kai/software/amber20_src/AmberTools/src/gem.pmemd/src/nextprmtop_section.F90
Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:
#0 0x7f0529341eea
#1 0x7f0529342a45
#2 0x7f05293431fc
#3 0x7f052940d6ae
#4 0x7f05294107f4
#5 0x563e9fe48999
#6 0x563e9fe62a6b
#7 0x563e9fe34fb5
#8 0x563e9fe61e95
#9 0x563e9fd7066e
#10 0x7f0528d3eb96
#11 0x563e9fd706a9
#12 0xffffffffffffffff
  ./Run.amoeba_formbox.pmemd.gem: Program error
Makefile:1607: recipe for target 'test.gem.pmemd.yes' failed
make[2]: [test.gem.pmemd.yes] Error 1 (已忽略)
cd amoeba_IL && ./Run.amoeba_IL.pmemd.gem
At line 104 of file /home/Kai/software/amber20_src/AmberTools/src/gem.pmemd/src/nextinpcrd_section.F90
Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:
#0 0x7f6a7b758eea
#1 0x7f6a7b759a45
#2 0x7f6a7b75a1fc
#3 0x7f6a7b8246ae
#4 0x7f6a7b8277f4
#5 0x561e8e5204e9
#6 0x561e8e4a5f25
#7 0x561e8e50debc
#8 0x561e8e53ae95
#9 0x561e8e44966e
#10 0x7f6a7b155b96
#11 0x561e8e4496a9
#12 0xffffffffffffffff
  ./Run.amoeba_IL.pmemd.gem: Program error
Makefile:1607: recipe for target 'test.gem.pmemd.yes' failed
make[2]: [test.gem.pmemd.yes] Error 1 (已忽略)
cd amoeba_jac3 && ./Run.jac_amba_beeman_MCbar.pmemd.gem
At line 104 of file /home/Kai/software/amber20_src/AmberTools/src/gem.pmemd/src/nextinpcrd_section.F90
Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:
#0 0x7fcc1eeffeea
#1 0x7fcc1ef00a45
#2 0x7fcc1ef011fc
#3 0x7fcc1efcb6ae
#4 0x7fcc1efce7f4
#5 0x55efc027d4e9
#6 0x55efc0202f25
#7 0x55efc026aebc
#8 0x55efc0297e95
#9 0x55efc01a666e
#10 0x7fcc1e8fcb96
#11 0x55efc01a66a9
#12 0xffffffffffffffff
  ./Run.jac_amba_beeman_MCbar.pmemd.gem: Program error
Makefile:1607: recipe for target 'test.gem.pmemd.yes' failed
make[2]: [test.gem.pmemd.yes] Error 1 (已忽略)
cd amoeba_jac3 && ./Run.jac_amba_beeman_nvt.pmemd.gem
At line 104 of file /home/Kai/software/amber20_src/AmberTools/src/gem.pmemd/src/nextinpcrd_section.F90
Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:
#0 0x7fa13abbdeea
#1 0x7fa13abbea45
#2 0x7fa13abbf1fc
#3 0x7fa13ac896ae
#4 0x7fa13ac8c7f4
#5 0x563b032924e9
#6 0x563b03217f25
#7 0x563b0327febc
#8 0x563b032ace95
#9 0x563b031bb66e
#10 0x7fa13a5bab96
#11 0x563b031bb6a9
#12 0xffffffffffffffff
  ./Run.jac_amba_beeman_nvt.pmemd.gem: Program error
Makefile:1607: recipe for target 'test.gem.pmemd.yes' failed
make[2]: [test.gem.pmemd.yes] Error 1 (已忽略)
cd amoeba_jac3 && ./Run.jac_amba_beeman_virial.pmemd.gem
At line 104 of file /home/Kai/software/amber20_src/AmberTools/src/gem.pmemd/src/nextinpcrd_section.F90
Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:
#0 0x7f65b6d66eea
#1 0x7f65b6d67a45
#2 0x7f65b6d681fc
#3 0x7f65b6e326ae
#4 0x7f65b6e357f4
#5 0x56354b5e54e9
#6 0x56354b56af25
#7 0x56354b5d2ebc
#8 0x56354b5ffe95
#9 0x56354b50e66e
#10 0x7f65b6763b96
#11 0x56354b50e6a9
#12 0xffffffffffffffff
  ./Run.jac_amba_beeman_virial.pmemd.gem: Program error
Makefile:1607: recipe for target 'test.gem.pmemd.yes' failed
make[2]: [test.gem.pmemd.yes] Error 1 (已忽略)
cd amoeba_jac3 && ./Run.jac_amba_verlet_nvt.pmemd.gem
At line 104 of file /home/Kai/software/amber20_src/AmberTools/src/gem.pmemd/src/nextinpcrd_section.F90
Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:
#0 0x7fad63a29eea
#1 0x7fad63a2aa45
#2 0x7fad63a2b1fc
#3 0x7fad63af56ae
#4 0x7fad63af87f4
#5 0x555aff9b34e9
#6 0x555aff938f25
#7 0x555aff9a0ebc
#8 0x555aff9cde95
#9 0x555aff8dc66e
#10 0x7fad63426b96
#11 0x555aff8dc6a9
#12 0xffffffffffffffff
  ./Run.jac_amba_verlet_nvt.pmemd.gem: Program error
Makefile:1607: recipe for target 'test.gem.pmemd.yes' failed
make[2]: [test.gem.pmemd.yes] Error 1 (已忽略)
cd amoeba_gb1 && ./Run.amoeba_gb1.pmemd.gem
At line 174 of file /home/Kai/software/amber20_src/AmberTools/src/gem.pmemd/src/nextprmtop_section.F90
Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:
#0 0x7f4f0f3dceea
#1 0x7f4f0f3dda45
#2 0x7f4f0f3de1fc
#3 0x7f4f0f4a86ae
#4 0x7f4f0f4ab7f4
#5 0x561b05c4c999
#6 0x561b05c66a6b
#7 0x561b05c38fb5
#8 0x561b05c65e95
#9 0x561b05b7466e
#10 0x7f4f0edd9b96
#11 0x561b05b746a9
#12 0xffffffffffffffff
  ./Run.amoeba_gb1.pmemd.gem: Program error
Makefile:1607: recipe for target 'test.gem.pmemd.yes' failed
make[2]: [test.gem.pmemd.yes] Error 1 (已忽略)
cd amoeba_wat1 && ./Run.amoeba_wat1.pmemd.gem
At line 174 of file /home/Kai/software/amber20_src/AmberTools/src/gem.pmemd/src/nextprmtop_section.F90
Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:
#0 0x7f8f35ad3eea
#1 0x7f8f35ad4a45
#2 0x7f8f35ad51fc
#3 0x7f8f35b9f6ae
#4 0x7f8f35ba27f4
#5 0x55e6dfd25999
#6 0x55e6dfd3fa6b
#7 0x55e6dfd11fb5
#8 0x55e6dfd3ee95
#9 0x55e6dfc4d66e
#10 0x7f8f354d0b96
#11 0x55e6dfc4d6a9
#12 0xffffffffffffffff
  ./Run.amoeba_wat1.pmemd.gem: Program error
Makefile:1607: recipe for target 'test.gem.pmemd.yes' failed
make[2]: [test.gem.pmemd.yes] Error 1 (已忽略)
cd amoeba_wat2 && ./Run.amoeba_wat2.ntpverlet.pmemd.gem
At line 174 of file /home/Kai/software/amber20_src/AmberTools/src/gem.pmemd/src/nextprmtop_section.F90
Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:
#0 0x7f31e50bfeea
#1 0x7f31e50c0a45
#2 0x7f31e50c11fc
#3 0x7f31e518b6ae
#4 0x7f31e518e7f4
#5 0x55d918b82999
#6 0x55d918b9ca6b
#7 0x55d918b6efb5
#8 0x55d918b9be95
#9 0x55d918aaa66e
#10 0x7f31e4abcb96
#11 0x55d918aaa6a9
#12 0xffffffffffffffff
  ./Run.amoeba_wat2.ntpverlet.pmemd.gem: Program error
Makefile:1607: recipe for target 'test.gem.pmemd.yes' failed
make[2]: [test.gem.pmemd.yes] Error 1 (已忽略)
cd amoeba_wat2 && ./Run.amoeba_wat2.pmemd.gem
At line 174 of file /home/Kai/software/amber20_src/AmberTools/src/gem.pmemd/src/nextprmtop_section.F90
Fortran runtime error: Bad value during floating point read

Error termination. Backtrace:
#0 0x7fea1143ceea
#1 0x7fea1143da45
#2 0x7fea1143e1fc
#3 0x7fea115086ae
#4 0x7fea1150b7f4
#5 0x561b7f52c999
#6 0x561b7f546a6b
#7 0x561b7f518fb5
#8 0x561b7f545e95
#9 0x561b7f45466e
#10 0x7fea10e39b96
#11 0x561b7f4546a9
#12 0xffffffffffffffff
  ./Run.amoeba_wat2.pmemd.gem: Program error
Makefile:1607: recipe for target 'test.gem.pmemd.yes' failed
make[2]: [test.gem.pmemd.yes] Error 1 (已忽略)
make[2]: 离开目录“/home/Kai/software/amber20/test”
make[2]: 进入目录“/home/Kai/software/amber20/AmberTools/test”

Finished test suite for AmberTools at 2020年 07月 21日 星期二 11:55:48 CST.

make[2]: 离开目录“/home/Kai/software/amber20/AmberTools/test”
1474 file comparisons passed
30 file comparisons failed (3 of which can be ignored)
594 tests experienced errors
Test log file saved as /home/Kai/software/amber20///logs/test_at_serial/2020-07-21_11-42-49.log
Test diffs file saved as /home/Kai/software/amber20///logs/test_at_serial/2020-07-21_11-42-49.diff

 Could anyone give us some suggestions to solve the problem? Thank you very much.

Best,
Geng
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Received on Tue Aug 18 2020 - 18:30:02 PDT
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