You are here

Cannot install DAlphaBall

2 posts / 0 new
Last post
Cannot install DAlphaBall
#1

I have an Ubuntu 22.04 system, and I am stuggling to install DAlphaBall. I have compiled the stable Rosetta version with hdf5 support, but when I do make on DAlphaBall I get the following:

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  -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
collect2: error: ld returned 1 exit status
make: *** [Makefile:77: DAlphaBall.gcc] Error 1

I tried with gcc-5 and with gcc4.8 with no avail. I guess the error means I have some problem in the Makefile at line 77, but line 77 is the follwoing:

     77         $(LD) -o $(NAMEFUL1) $(LDFLAGS) $(OBJECTS1) $(LIBS) $(LIBRARIES)

Which does not mean a lot to me.

Any ideas?

 

Category: 
Post Situation: 
Fri, 2023-10-13 07:55
gerdos

 

Hello, I encountered a similar error while attempting to install DAlphaBall on my Ubuntu 22.04 system.

I resolved these issues by referring to the following website:

https://github.com/outpace-bio/DAlphaBall#tldr

 

$ git clone https://github.com/outpace-bio/DAlphaBall.git

$ dalphaball_docker_build.sh ../tmt/

# at 'DAlphaBall/src'

$ make

 

I hope this helps you

Fri, 2023-11-24 04:52
Seongsung