I have two servers with exactly the same hardware and software configurations. One of them processing WU's just fine, the other shows no CPU usage under htop and all of the boinc processes show up as defunct or zombies.

Such as:

boinc 28765 6.6 1.7 342320 285388 ? SNl 14:04 0:19 ../../projects/boinc.bakerlab.org_rosetta/minirosetta_3.14_x86_64-pc-linux-gnu @monomer_all_boinc_1lu9B_127.nonlocal.pctid_0.09.tmscore_0.23359._nonlocal_tex.boinc.flags -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip monomer_all_boinc_1lu9B_127.nonlocal.pctid_0.09.tmscore_0.23359._nonlocal_tex.boinc.zip -nstruct 10000 -cpu_run_time 10800 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3286016
boinc 28794 6.7 0.0 0 0 ? ZN 14:04 0:20 [minirosetta_3.1] <defunct>

I have two servers with exactly the same hardware and software configurations. One of them processing WU's just fine, the other shows no CPU usage under htop and all of the boinc processes show up as defunct or zombies.

Such as:

boinc 28765 6.6 1.7 342320 285388 ? SNl 14:04 0:19 ../../projects/boinc.bakerlab.org_rosetta/minirosetta_3.14_x86_64-pc-linux-gnu @monomer_all_boinc_1lu9B_127.nonlocal.pctid_0.09.tmscore_0.23359._nonlocal_tex.boinc.flags -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip monomer_all_boinc_1lu9B_127.nonlocal.pctid_0.09.tmscore_0.23359._nonlocal_tex.boinc.zip -nstruct 10000 -cpu_run_time 10800 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3286016
boinc 28794 6.7 0.0 0 0 ? ZN 14:04 0:20 [minirosetta_3.1] <defunct>

No clue but since it is a Linux Server you might want to ask in the Linux section.