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Protein hallucination and inpainting with RoseTTAFold
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error while running Rifdock protocol #57

Closed anneday closed 7 months ago

anneday commented 8 months ago

When I ran Step 12 in Cao protocol for binder design, I prepared paper_interface_design_pilot_commands. List when I did RIFdocking step 12 Running a pilot job. But when I ran commands in the list, Dalphaball reports error below: protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN METRIC sap_score======================= basic.io.database: Database file opened: scoring/score_functions/sap_sasa_calib.dat WARNING!! DALPHABALL output nan at index 140724834832176 DALPHABALL output indicies not matching! 1!=140724834832176

ERROR:: Exit from: src/core/scoring/packing/surf_vol.cc line: 170 protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:

File: src/core/scoring/packing/surf_vol.cc:170 [ ERROR ] UtilityExitException ERROR:

protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job ferr_hh_00251_000000134_0001

[ ERROR ]: Caught exception:

File: src/core/scoring/packing/surf_vol.cc:170 [ ERROR ] UtilityExitException ERROR:

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

protocols.jd2.JobDistributor: [ WARNING ] ferr_hh_00251_000000134_0001 reported failure and will NOT retry protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 20 jobs considered, 20 jobs attempted in 6349 seconds. It seems that the error is caused by Dalphaball. And when I compiled Dalphaball in rosetta 3.13 with gcc 11.04: gcc -o ./DAlphaBall.gcc -O3 DAlphaBall.o sos_minor_gmp.o alf_tools_gmp.o binding.o adjust.o alfcx.o alfcx_tools.o cavballs.o delcx.o truncate_real.o measure_tools.o surface_tools.o surface_only.o surface_deriv_coord.o volume_tools.o volume_only.o volume_deriv_coord.o vector.o write_simplices.o -L/usr/local/lib -lgmp -lm -lgfortran /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1e85be0): multiple definition of coord_gmp'; sos_minor_gmp.o:(.bss+0x1e85be0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xb80): multiple definition ofa_mp'; sos_minor_gmp.o:(.bss+0xb80): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xb20): multiple definition of b_mp'; sos_minor_gmp.o:(.bss+0xb20): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xac0): multiple definition ofc_mp'; sos_minor_gmp.o:(.bss+0xac0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x13e0): multiple definition of weight_gmp'; sos_minor_gmp.o:(.bss+0x13e0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1280): multiple definition oftemp1'; sos_minor_gmp.o:(.bss+0x1280): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1270): multiple definition of temp2'; sos_minor_gmp.o:(.bss+0x1270): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x480): multiple definition ofMab'; sos_minor_gmp.o:(.bss+0x480): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x340): multiple definition of Mac'; sos_minor_gmp.o:(.bss+0x340): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x200): multiple definition ofMbc'; sos_minor_gmp.o:(.bss+0x200): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xc0): multiple definition of S'; sos_minor_gmp.o:(.bss+0xc0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x0): multiple definition ofT'; sos_minor_gmp.o:(.bss+0x0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xf30): multiple definition of Dabc'; sos_minor_gmp.o:(.bss+0xf30): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x980): multiple definition ofDab'; sos_minor_gmp.o:(.bss+0x980): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x9e0): multiple definition of Sab'; sos_minor_gmp.o:(.bss+0x9e0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xa20): multiple definition ofTab'; sos_minor_gmp.o:(.bss+0xa20): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xa60): multiple definition of d_mp'; sos_minor_gmp.o:(.bss+0xa60): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xee0): multiple definition ofwa'; sos_minor_gmp.o:(.bss+0xee0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xed0): multiple definition of wb'; sos_minor_gmp.o:(.bss+0xed0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xec0): multiple definition ofwc'; sos_minor_gmp.o:(.bss+0xec0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xeb0): multiple definition of wd'; sos_minor_gmp.o:(.bss+0xeb0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xf437e0): multiple definition ofradius_gmp'; sos_minor_gmp.o:(.bss+0xf437e0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xea0): multiple definition of ra_mp'; sos_minor_gmp.o:(.bss+0xea0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xe90): multiple definition ofrb_mp'; sos_minor_gmp.o:(.bss+0xe90): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xe80): multiple definition of rc_mp'; sos_minor_gmp.o:(.bss+0xe80): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xe70): multiple definition ofrd_mp'; sos_minor_gmp.o:(.bss+0xe70): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xe60): multiple definition of alp'; sos_minor_gmp.o:(.bss+0xe60): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x940): multiple definition ofSac'; sos_minor_gmp.o:(.bss+0x940): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x900): multiple definition of Sad'; sos_minor_gmp.o:(.bss+0x900): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x8c0): multiple definition ofSbc'; sos_minor_gmp.o:(.bss+0x8c0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x880): multiple definition of Sbd'; sos_minor_gmp.o:(.bss+0x880): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x840): multiple definition ofScd'; sos_minor_gmp.o:(.bss+0x840): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1260): multiple definition of temp3'; sos_minor_gmp.o:(.bss+0x1260): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x800): multiple definition ofSa'; sos_minor_gmp.o:(.bss+0x800): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x7c0): multiple definition of Sb'; sos_minor_gmp.o:(.bss+0x7c0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x5c0): multiple definition ofSc'; sos_minor_gmp.o:(.bss+0x5c0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x780): multiple definition of Sd'; sos_minor_gmp.o:(.bss+0x780): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x640): multiple definition ofDeter'; sos_minor_gmp.o:(.bss+0x640): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x740): multiple definition of Sam1'; sos_minor_gmp.o:(.bss+0x740): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x700): multiple definition ofSbm1'; sos_minor_gmp.o:(.bss+0x700): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x6c0): multiple definition of Scm1'; sos_minor_gmp.o:(.bss+0x6c0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x680): multiple definition ofSdm1'; sos_minor_gmp.o:(.bss+0x680): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xf70): multiple definition of det1'; sos_minor_gmp.o:(.bss+0xf70): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xf60): multiple definition ofdet2'; sos_minor_gmp.o:(.bss+0xf60): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xf40): multiple definition of det4'; sos_minor_gmp.o:(.bss+0xf40): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xf50): multiple definition ofdet3'; sos_minor_gmp.o:(.bss+0xf50): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xf20): multiple definition of Dabd'; sos_minor_gmp.o:(.bss+0xf20): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xf10): multiple definition ofDacd'; sos_minor_gmp.o:(.bss+0xf10): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xf00): multiple definition of Dbcd'; sos_minor_gmp.o:(.bss+0xf00): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xef0): multiple definition ofDabcd'; sos_minor_gmp.o:(.bss+0xef0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1000): multiple definition of den'; sos_minor_gmp.o:(.bss+0x1000): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1010): multiple definition ofnum'; sos_minor_gmp.o:(.bss+0x1010): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1030): multiple definition of dist2'; sos_minor_gmp.o:(.bss+0x1030): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1040): multiple definition ofrb2'; sos_minor_gmp.o:(.bss+0x1040): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1050): multiple definition of ra2'; sos_minor_gmp.o:(.bss+0x1050): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1020): multiple definition ofdtest'; sos_minor_gmp.o:(.bss+0x1020): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x600): multiple definition of Tc'; sos_minor_gmp.o:(.bss+0x600): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xbe0): multiple definition ofres2_c'; sos_minor_gmp.o:(.bss+0xbe0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xd20): multiple definition of res'; sos_minor_gmp.o:(.bss+0xd20): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xff0): multiple definition ofr_11'; sos_minor_gmp.o:(.bss+0xff0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xfe0): multiple definition of r_22'; sos_minor_gmp.o:(.bss+0xfe0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xfd0): multiple definition ofr_33'; sos_minor_gmp.o:(.bss+0xfd0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xf90): multiple definition of diff'; sos_minor_gmp.o:(.bss+0xf90): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xf80): multiple definition ofdet0'; sos_minor_gmp.o:(.bss+0xf80): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xfc0): multiple definition of r_14'; sos_minor_gmp.o:(.bss+0xfc0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xfb0): multiple definition ofr_313'; sos_minor_gmp.o:(.bss+0xfb0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0xfa0): multiple definition of r_212'; sos_minor_gmp.o:(.bss+0xfa0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1060): multiple definition ofg3'; sos_minor_gmp.o:(.bss+0x1060): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1070): multiple definition of g2'; sos_minor_gmp.o:(.bss+0x1070): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1080): multiple definition ofg1'; sos_minor_gmp.o:(.bss+0x1080): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1090): multiple definition of f3'; sos_minor_gmp.o:(.bss+0x1090): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x10a0): multiple definition off2'; sos_minor_gmp.o:(.bss+0x10a0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x10b0): multiple definition of f1'; sos_minor_gmp.o:(.bss+0x10b0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x10c0): multiple definition ofe3'; sos_minor_gmp.o:(.bss+0x10c0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x10d0): multiple definition of e2'; sos_minor_gmp.o:(.bss+0x10d0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x10e0): multiple definition ofe1'; sos_minor_gmp.o:(.bss+0x10e0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x10f0): multiple definition of d3'; sos_minor_gmp.o:(.bss+0x10f0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1100): multiple definition ofd2'; sos_minor_gmp.o:(.bss+0x1100): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1110): multiple definition of d1'; sos_minor_gmp.o:(.bss+0x1110): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1120): multiple definition ofc44'; sos_minor_gmp.o:(.bss+0x1120): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1130): multiple definition of c43'; sos_minor_gmp.o:(.bss+0x1130): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1140): multiple definition ofc42'; sos_minor_gmp.o:(.bss+0x1140): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1150): multiple definition of c41'; sos_minor_gmp.o:(.bss+0x1150): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1160): multiple definition ofc34'; sos_minor_gmp.o:(.bss+0x1160): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1170): multiple definition of c33'; sos_minor_gmp.o:(.bss+0x1170): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1180): multiple definition ofc32'; sos_minor_gmp.o:(.bss+0x1180): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1190): multiple definition of c31'; sos_minor_gmp.o:(.bss+0x1190): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x11a0): multiple definition ofc24'; sos_minor_gmp.o:(.bss+0x11a0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x11b0): multiple definition of c23'; sos_minor_gmp.o:(.bss+0x11b0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x11c0): multiple definition ofc22'; sos_minor_gmp.o:(.bss+0x11c0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x11d0): multiple definition of c21'; sos_minor_gmp.o:(.bss+0x11d0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x11e0): multiple definition ofc14'; sos_minor_gmp.o:(.bss+0x11e0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x11f0): multiple definition of c13'; sos_minor_gmp.o:(.bss+0x11f0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1200): multiple definition ofc12'; sos_minor_gmp.o:(.bss+0x1200): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1210): multiple definition of c11'; sos_minor_gmp.o:(.bss+0x1210): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1220): multiple definition ofval3'; sos_minor_gmp.o:(.bss+0x1220): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1230): multiple definition of val2'; sos_minor_gmp.o:(.bss+0x1230): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1240): multiple definition ofval1'; sos_minor_gmp.o:(.bss+0x1240): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1250): multiple definition of temp4'; sos_minor_gmp.o:(.bss+0x1250): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1290): multiple definition ofa54_mp'; sos_minor_gmp.o:(.bss+0x1290): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x12a0): multiple definition of a53_mp'; sos_minor_gmp.o:(.bss+0x12a0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x12b0): multiple definition ofa52_mp'; sos_minor_gmp.o:(.bss+0x12b0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x12c0): multiple definition of a51_mp'; sos_minor_gmp.o:(.bss+0x12c0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x12d0): multiple definition ofa44_mp'; sos_minor_gmp.o:(.bss+0x12d0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x12e0): multiple definition of a43_mp'; sos_minor_gmp.o:(.bss+0x12e0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x12f0): multiple definition ofa42_mp'; sos_minor_gmp.o:(.bss+0x12f0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1300): multiple definition of a41_mp'; sos_minor_gmp.o:(.bss+0x1300): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1310): multiple definition ofa34_mp'; sos_minor_gmp.o:(.bss+0x1310): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1320): multiple definition of a33_mp'; sos_minor_gmp.o:(.bss+0x1320): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1330): multiple definition ofa32_mp'; sos_minor_gmp.o:(.bss+0x1330): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1340): multiple definition of a31_mp'; sos_minor_gmp.o:(.bss+0x1340): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1350): multiple definition ofa24_mp'; sos_minor_gmp.o:(.bss+0x1350): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1360): multiple definition of a23_mp'; sos_minor_gmp.o:(.bss+0x1360): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1370): multiple definition ofa22_mp'; sos_minor_gmp.o:(.bss+0x1370): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1380): multiple definition of a21_mp'; sos_minor_gmp.o:(.bss+0x1380): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x1390): multiple definition ofa14_mp'; sos_minor_gmp.o:(.bss+0x1390): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x13a0): multiple definition of a13_mp'; sos_minor_gmp.o:(.bss+0x13a0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x13b0): multiple definition ofa12_mp'; sos_minor_gmp.o:(.bss+0x13b0): first defined here /usr/bin/ld: alf_tools_gmp.o:(.bss+0x13c0): multiple definition of `a11_mp'; sos_minor_gmp.o:(.bss+0x13c0): first defined here Could anyone tell me how to solve this?Please! Thank you so much!

roccomoretti commented 7 months ago

This sounds like a similar issue to the one posted on the RosettaCommons Forums. -- In summary, you need to use an earlier GCC version (like ~6.3) to compile Dalphaball. Also, you should double-check the settings of your -dalphaball option to make sure you're pointing to the proper Dalphaball executable.

At any rate, your issues here are unrelated to the RFDesign application proper, so if you have further questions about this issue, I'd encourage you to post at the RosettaCommons Forums.