Can you try with a 48 bit affinity mask to see what that does?
--cpu-affinity 0xffffffffffff
Using --cpu-affinity 0xffffffffffff makes it correctly run on 48 CPUs:
# ./cpuminer -c conf.conf -q -D --cpu-affinity 0xffffffffffff
********** cpuminer-opt 3.7.6 ***********
A CPU miner with multi algo support and optimized for CPUs
with AES_NI and AVX2 and SHA extensions.
BTC donation address: 12tdvfF7KmAsihBXQXynT6E6th2c2pByTT
CPU: AMD EPYC 7401P 24-Core Processor .
SW built on Dec 16 2017 with GCC 5.4.0.
CPU features: SSE2 AES AVX AVX2 SHA.
SW features: SSE2 AES AVX AVX2 SHA.
Algo features: AVX AVX2.
Start mining with AVX2.
[2017-12-16 02:19:58] Starting Stratum on stratum+tcp://pool:80
[2017-12-16 02:19:58] Binding thread 0 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 1 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 2 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 3 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 4 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 5 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 6 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 7 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 8 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 9 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 10 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 11 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 12 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 13 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 14 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 15 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 16 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 17 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 18 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 19 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 20 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 21 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 22 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 23 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 24 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 25 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 26 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 27 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 28 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 29 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 30 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 31 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 33 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 32 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 34 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 35 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 36 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 37 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 38 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 39 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 40 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 41 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 42 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 43 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 44 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 45 to cpu mask ffffffff
[2017-12-16 02:19:58] Binding thread 46 to cpu mask ffffffff
[2017-12-16 02:19:58] 48 miner threads started, using 'lyra2z' algorithm.
[2017-12-16 02:19:58] Binding thread 47 to cpu mask ffffffff
[2017-12-16 02:19:59] Stratum session id: deadbeefcafebabe61fe000000000000
[2017-12-16 02:19:59] Stratum difficulty set to 10
[2017-12-16 02:20:00] Stratum difficulty set to 5
[2017-12-16 02:20:00] DEBUG: job_id='1ea2' extranonce2=00000000 ntime=5a34829d
[2017-12-16 02:20:00] Stratum difficulty set to 10 (0.03906)
[2017-12-16 02:20:04] DEBUG: job_id='1ea3' extranonce2=00000000 ntime=5a3482d4
[2017-12-16 02:20:04] Stratum difficulty set to 5 (0.01953)
(...)
If we don't use --cpu-affinity 0xffffffffffff, it runs on 32 CPUs (as observed in htop or top - it still fires 48 threads though):
# ./cpuminer -c conf.conf -q -D
********** cpuminer-opt 3.7.6 ***********
A CPU miner with multi algo support and optimized for CPUs
with AES_NI and AVX2 and SHA extensions.
BTC donation address: 12tdvfF7KmAsihBXQXynT6E6th2c2pByTT
CPU: AMD EPYC 7401P 24-Core Processor .
SW built on Dec 16 2017 with GCC 5.4.0.
CPU features: SSE2 AES AVX AVX2 SHA.
SW features: SSE2 AES AVX AVX2 SHA.
Algo features: AVX AVX2.
Start mining with AVX2.
[2017-12-16 02:22:34] Starting Stratum on stratum+tcp://pool:80
[2017-12-16 02:22:34] Binding thread 0 to cpu 0 (mask 1)
[2017-12-16 02:22:34] Binding thread 1 to cpu 1 (mask 2)
[2017-12-16 02:22:34] Binding thread 2 to cpu 2 (mask 4)
[2017-12-16 02:22:34] Binding thread 3 to cpu 3 (mask 8)
[2017-12-16 02:22:34] Binding thread 4 to cpu 4 (mask 10)
[2017-12-16 02:22:34] Binding thread 5 to cpu 5 (mask 20)
[2017-12-16 02:22:34] Binding thread 6 to cpu 6 (mask 40)
[2017-12-16 02:22:34] Binding thread 7 to cpu 7 (mask 80)
[2017-12-16 02:22:34] Binding thread 8 to cpu 8 (mask 100)
[2017-12-16 02:22:34] Binding thread 9 to cpu 9 (mask 200)
[2017-12-16 02:22:34] Binding thread 10 to cpu 10 (mask 400)
[2017-12-16 02:22:34] Binding thread 11 to cpu 11 (mask 800)
[2017-12-16 02:22:34] Binding thread 12 to cpu 12 (mask 1000)
[2017-12-16 02:22:34] Binding thread 13 to cpu 13 (mask 2000)
[2017-12-16 02:22:34] Binding thread 14 to cpu 14 (mask 4000)
[2017-12-16 02:22:34] Binding thread 15 to cpu 15 (mask 8000)
[2017-12-16 02:22:34] Binding thread 16 to cpu 16 (mask 10000)
[2017-12-16 02:22:34] Binding thread 17 to cpu 17 (mask 20000)
[2017-12-16 02:22:34] Binding thread 18 to cpu 18 (mask 40000)
[2017-12-16 02:22:34] Binding thread 19 to cpu 19 (mask 80000)
[2017-12-16 02:22:34] Binding thread 20 to cpu 20 (mask 100000)
[2017-12-16 02:22:34] Binding thread 21 to cpu 21 (mask 200000)
[2017-12-16 02:22:34] Binding thread 22 to cpu 22 (mask 400000)
[2017-12-16 02:22:34] Binding thread 23 to cpu 23 (mask 800000)
[2017-12-16 02:22:34] Binding thread 24 to cpu 24 (mask 1000000)
[2017-12-16 02:22:34] Binding thread 25 to cpu 25 (mask 2000000)
[2017-12-16 02:22:34] Binding thread 26 to cpu 26 (mask 4000000)
[2017-12-16 02:22:34] Binding thread 27 to cpu 27 (mask 8000000)
[2017-12-16 02:22:34] Binding thread 28 to cpu 28 (mask 10000000)
[2017-12-16 02:22:34] Binding thread 29 to cpu 29 (mask 20000000)
[2017-12-16 02:22:34] Binding thread 30 to cpu 30 (mask 40000000)
[2017-12-16 02:22:34] Binding thread 31 to cpu 31 (mask 80000000)
[2017-12-16 02:22:34] Binding thread 32 to cpu 32 (mask 1)
[2017-12-16 02:22:34] Binding thread 33 to cpu 33 (mask 2)
[2017-12-16 02:22:34] Binding thread 34 to cpu 34 (mask 4)
[2017-12-16 02:22:34] Binding thread 35 to cpu 35 (mask 8)
[2017-12-16 02:22:34] Binding thread 36 to cpu 36 (mask 10)
[2017-12-16 02:22:34] Binding thread 37 to cpu 37 (mask 20)
[2017-12-16 02:22:34] Binding thread 38 to cpu 38 (mask 40)
[2017-12-16 02:22:34] Binding thread 39 to cpu 39 (mask 80)
[2017-12-16 02:22:34] Binding thread 40 to cpu 40 (mask 100)
[2017-12-16 02:22:34] Binding thread 41 to cpu 41 (mask 200)
[2017-12-16 02:22:34] Binding thread 42 to cpu 42 (mask 400)
[2017-12-16 02:22:34] Binding thread 43 to cpu 43 (mask 800)
[2017-12-16 02:22:34] Binding thread 44 to cpu 44 (mask 1000)
[2017-12-16 02:22:34] Binding thread 45 to cpu 45 (mask 2000)
[2017-12-16 02:22:34] Binding thread 46 to cpu 46 (mask 4000)
[2017-12-16 02:22:34] 48 miner threads started, using 'lyra2z' algorithm.
[2017-12-16 02:22:34] Binding thread 47 to cpu 47 (mask 8000)
[2017-12-16 02:22:35] Stratum session id: deadbeefcafebabec147160000000000
[2017-12-16 02:22:35] Stratum difficulty set to 10
[2017-12-16 02:22:36] Stratum difficulty set to 5
[2017-12-16 02:22:36] DEBUG: job_id='1e9f' extranonce2=00000000 ntime=5a348344
[2017-12-16 02:22:36] Stratum difficulty set to 10 (0.03906)
[2017-12-16 02:22:52] DEBUG: job_id='1ea0' extranonce2=00000000 ntime=5a34837b
[2017-12-16 02:22:52] Stratum difficulty set to 5 (0.01953)
(...)