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Dimensionality reduction show error #1

Open Paulie-ai opened 1 year ago

Paulie-ai commented 1 year ago

Hello, When i execute command plumed driver --mf_pdb traj.pdb with plumed_ex2.dat file and I encounter error with in pca part: DRIVER: Found molfile format trajectory pdb with name traj.pdb PLUMED: PLUMED is starting PLUMED: Version: 2.9.0 (git: Unknown) compiled on Jun 17 2023 at 20:24:06 PLUMED: Please cite these papers when using PLUMED [1][2] PLUMED: For further information see the PLUMED web page at http://www.plumed.org PLUMED: Root: /home/paulie/software/plumed290/lib/plumed PLUMED: For installed feature, see /home/paulie/software/plumed290/lib/plumed/src/config/config.txt PLUMED: Molecular dynamics engine: driver PLUMED: Precision of reals: 8 PLUMED: Running over 1 node PLUMED: Number of threads: 1 PLUMED: Cache line size: 512 PLUMED: Number of atoms: 256 PLUMED: File suffix: PLUMED: FILE: plumed.dat PLUMED: Action MOLINFO PLUMED: with label @0 PLUMED: pdb file named bhp.pdb contains 1 chains PLUMED: chain named contains residues 1 to 18 and atoms 1 to 256 PLUMED: Action COLLECT_FRAMES PLUMED: with label cc PLUMED: with stride 1 PLUMED: doing calculation in serial PLUMED: monitoring positions of atoms 2 5 6 7 9 12 13 14 16 18 21 24 25 26 27 28 29 31 33 36 37 39 41 42 44 46 48 50 51 52 53 55 57 59 63 65 66 67 69 71 74 75 77 79 80 82 84 86 87 88 90 92 95 96 97 98 99 100 102 104 107 108 109 110 111 112 114 116 120 121 122 124 126 128 132 134 135 136 138 140 143 146 149 152 156 157 158 160 162 164 168 170 171 172 174 176 179 180 182 184 186 188 190 191 192 194 196 198 202 204 205 206 208 210 212 216 220 221 222 224 226 228 232 234 235 236 238 240 243 246 247 248 249 250 251 253 PLUMED: weights are all equal to one PLUMED: ERROR PLUMED: I cannot understand line: PCA LABEL=pca USE_OUTPUT_DATA_FROM=cc METRIC=OPTIMAL NLOW_DIM=2 PLUMED: Maybe a missing space or a typo? PLUMED: ################################################################################ PLUMED: PLUMED: (core/PlumedMain.cpp:823) void PLMD::PlumedMain::readInputWords(const std::vector<std::__cxx11::basic_string >&) PLUMED: ERROR PLUMED: I cannot understand line: PCA LABEL=pca USE_OUTPUT_DATA_FROM=cc METRIC=OPTIMAL NLOW_DIM=2 PLUMED: Maybe a missing space or a typo? PLUMED: ################################################################################ PLUMED: Cycles Total Average Minimum Maximum PLUMED: 1 0.002229 0.002229 0.002229 0.002229 terminate called after throwing an instance of 'PLMD::Plumed::ExceptionError' what(): (core/PlumedMain.cpp:823) void PLMD::PlumedMain::readInputWords(const std::vector<std::__cxx11::basic_string >&) ERROR I cannot understand line: PCA LABEL=pca USE_OUTPUT_DATA_FROM=cc METRIC=OPTIMAL NLOW_DIM=2 Maybe a missing space or a typo? Aborted (core dumped)

How can i fixed this error, thanks.

gtribello commented 1 year ago

Reconfigure and recompile plumed. When you reconfigure use

./configure --enable-modules=all

Hope this helps

Gareth

On Sun, 18 Jun 2023, 10:37 L&S, @.***> wrote:

Hello, When i execute command plumed driver --mf_pdb traj.pdb with plumed_ex2.dat file and I encounter error with in pca part: DRIVER: Found molfile format trajectory pdb with name traj.pdb PLUMED: PLUMED is starting PLUMED: Version: 2.9.0 (git: Unknown) compiled on Jun 17 2023 at 20:24:06 PLUMED: Please cite these papers when using PLUMED [1][2] PLUMED: For further information see the PLUMED web page at http://www.plumed.org PLUMED: Root: /home/paulie/software/plumed290/lib/plumed PLUMED: For installed feature, see /home/paulie/software/plumed290/lib/plumed/src/config/config.txt PLUMED: Molecular dynamics engine: driver PLUMED: Precision of reals: 8 PLUMED: Running over 1 node PLUMED: Number of threads: 1 PLUMED: Cache line size: 512 PLUMED: Number of atoms: 256 PLUMED: File suffix: PLUMED: FILE: plumed.dat PLUMED: Action MOLINFO PLUMED: with label @0 https://github.com/0 PLUMED: pdb file named bhp.pdb contains 1 chains PLUMED: chain named contains residues 1 to 18 and atoms 1 to 256 PLUMED: Action COLLECT_FRAMES PLUMED: with label cc PLUMED: with stride 1 PLUMED: doing calculation in serial PLUMED: monitoring positions of atoms 2 5 6 7 9 12 13 14 16 18 21 24 25 26 27 28 29 31 33 36 37 39 41 42 44 46 48 50 51 52 53 55 57 59 63 65 66 67 69 71 74 75 77 79 80 82 84 86 87 88 90 92 95 96 97 98 99 100 102 104 107 108 109 110 111 112 114 116 120 121 122 124 126 128 132 134 135 136 138 140 143 146 149 152 156 157 158 160 162 164 168 170 171 172 174 176 179 180 182 184 186 188 190 191 192 194 196 198 202 204 205 206 208 210 212 216 220 221 222 224 226 228 232 234 235 236 238 240 243 246 247 248 249 250 251 253 PLUMED: weights are all equal to one PLUMED: ERROR PLUMED: I cannot understand line: PCA LABEL=pca USE_OUTPUT_DATA_FROM=cc METRIC=OPTIMAL NLOW_DIM=2 PLUMED: Maybe a missing space or a typo? PLUMED: ################################################################################ PLUMED: PLUMED: (core/PlumedMain.cpp:823) void PLMD::PlumedMain::readInputWords(const std::vector&) PLUMED: ERROR PLUMED: I cannot understand line: PCA LABEL=pca USE_OUTPUT_DATA_FROM=cc METRIC=OPTIMAL NLOW_DIM=2 PLUMED: Maybe a missing space or a typo? PLUMED: ################################################################################ PLUMED: Cycles Total Average Minimum Maximum PLUMED: 1 0.002229 0.002229 0.002229 0.002229 terminate called after throwing an instance of 'PLMD::Plumed::ExceptionError' what(): (core/PlumedMain.cpp:823) void PLMD::PlumedMain::readInputWords(const std::vector&) ERROR I cannot understand line: PCA LABEL=pca USE_OUTPUT_DATA_FROM=cc METRIC=OPTIMAL NLOW_DIM=2 Maybe a missing space or a typo? Aborted (core dumped)

How can i fixed this error, thanks.

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Paulie-ai commented 1 year ago

Thanks for your reply, it fixed when complie with --enable-modules=all.

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------------------ 原始邮件 ------------------ 发件人: "plumed/masterclass-21-6" @.>; 发送时间: 2023年6月18日(星期天) 下午5:58 @.>; @.**@.>; 主题: Re: [plumed/masterclass-21-6] Dimensionality reduction show error (Issue #1)

Reconfigure and recompile plumed. When you reconfigure use

./configure --enable-modules=all

Hope this helps

Gareth

On Sun, 18 Jun 2023, 10:37 L&S, @.***> wrote:

> Hello, When i execute command plumed driver --mf_pdb traj.pdb with > plumed_ex2.dat file and I encounter error with in pca part: > DRIVER: Found molfile format trajectory pdb with name traj.pdb > PLUMED: PLUMED is starting > PLUMED: Version: 2.9.0 (git: Unknown) compiled on Jun 17 2023 at 20:24:06 > PLUMED: Please cite these papers when using PLUMED [1][2] > PLUMED: For further information see the PLUMED web page at > http://www.plumed.org > PLUMED: Root: /home/paulie/software/plumed290/lib/plumed > PLUMED: For installed feature, see > /home/paulie/software/plumed290/lib/plumed/src/config/config.txt > PLUMED: Molecular dynamics engine: driver > PLUMED: Precision of reals: 8 > PLUMED: Running over 1 node > PLUMED: Number of threads: 1 > PLUMED: Cache line size: 512 > PLUMED: Number of atoms: 256 > PLUMED: File suffix: > PLUMED: FILE: plumed.dat > PLUMED: Action MOLINFO > PLUMED: with label @0 <https://github.com/0&gt; > PLUMED: pdb file named bhp.pdb contains 1 chains > PLUMED: chain named contains residues 1 to 18 and atoms 1 to 256 > PLUMED: Action COLLECT_FRAMES > PLUMED: with label cc > PLUMED: with stride 1 > PLUMED: doing calculation in serial > PLUMED: monitoring positions of atoms 2 5 6 7 9 12 13 14 16 18 21 24 25 26 > 27 28 29 31 33 36 37 39 41 42 44 46 48 50 51 52 53 55 57 59 63 65 66 67 69 > 71 74 75 77 79 80 82 84 86 87 88 90 92 95 96 97 98 99 100 102 104 107 108 > 109 110 111 112 114 116 120 121 122 124 126 128 132 134 135 136 138 140 143 > 146 149 152 156 157 158 160 162 164 168 170 171 172 174 176 179 180 182 184 > 186 188 190 191 192 194 196 198 202 204 205 206 208 210 212 216 220 221 222 > 224 226 228 232 234 235 236 238 240 243 246 247 248 249 250 251 253 > PLUMED: weights are all equal to one > PLUMED: ERROR > PLUMED: I cannot understand line: PCA LABEL=pca USE_OUTPUT_DATA_FROM=cc > METRIC=OPTIMAL NLOW_DIM=2 > PLUMED: Maybe a missing space or a typo? > PLUMED: > ################################################################################ > PLUMED: > PLUMED: (core/PlumedMain.cpp:823) void > PLMD::PlumedMain::readInputWords(const > std::vector<std::__cxx11::basic_string >&) > PLUMED: ERROR > PLUMED: I cannot understand line: PCA LABEL=pca USE_OUTPUT_DATA_FROM=cc > METRIC=OPTIMAL NLOW_DIM=2 > PLUMED: Maybe a missing space or a typo? > PLUMED: > ################################################################################ > PLUMED: Cycles Total Average Minimum Maximum > PLUMED: 1 0.002229 0.002229 0.002229 0.002229 > terminate called after throwing an instance of > 'PLMD::Plumed::ExceptionError' > what(): > (core/PlumedMain.cpp:823) void PLMD::PlumedMain::readInputWords(const > std::vector<std::__cxx11::basic_string >&) > ERROR > I cannot understand line: PCA LABEL=pca USE_OUTPUT_DATA_FROM=cc > METRIC=OPTIMAL NLOW_DIM=2 > Maybe a missing space or a typo? > Aborted (core dumped) > > How can i fixed this error, thanks. > > — > Reply to this email directly, view it on GitHub > <https://github.com/plumed/masterclass-21-6/issues/1&gt;, or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ABC6P5HAUYHIVNH7HFHGUH3XL3D7HANCNFSM6AAAAAAZKY4L5A&gt; > . > You are receiving this because you are subscribed to this thread.Message > ID: @.***> >

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