error while running Rifdock protocol
anneday opened this issue · 1 comments
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 of a_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 of c_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 of temp1'; 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 of Mab'; 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 of Mbc'; 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 of T'; 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 of Dab'; 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 of Tab'; 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 of wa'; 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 of wc'; 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 of radius_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 of rb_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 of rd_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 of Sac'; 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 of Sbc'; 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 of Scd'; 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 of Sa'; 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 of Sc'; 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 of Deter'; 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 of Sbm1'; 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 of Sdm1'; 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 of det2'; 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 of det3'; 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 of Dacd'; 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 of Dabcd'; 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 of num'; 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 of rb2'; 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 of dtest'; 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 of res2_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 of r_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 of r_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 of det0'; 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 of r_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 of g3'; 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 of g1'; 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 of f2'; 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 of e3'; 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 of e1'; 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 of d2'; 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 of c44'; 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 of c42'; 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 of c34'; 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 of c32'; 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 of c24'; 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 of c22'; 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 of c14'; 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 of c12'; 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 of val3'; 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 of val1'; 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 of a54_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 of a52_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 of a44_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 of a42_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 of a34_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 of a32_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 of a24_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 of a22_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 of a14_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 of a12_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!
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.