From 35537c46a00c33db96409ce6aea42a42224f7917 Mon Sep 17 00:00:00 2001
From: Milot Mirdita <milot@mirdita.de>
Date: Tue, 7 Jan 2025 19:36:56 +0900
Subject: [PATCH] Make sure cuda binaries do not depend on dynamic libatomic

This would require a non glibc dependency installed
---
 azure-pipelines.yml | 13 +++++++++----
 src/CMakeLists.txt  | 21 +++++++++++++++------
 2 files changed, 24 insertions(+), 10 deletions(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 5df2017b..fe00b8b1 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -150,19 +150,24 @@ jobs:
       - script: |
           mkdir build && cd build
           export CC=gcc-10 ; export CXX=g++-10; export CUDAHOSTCXX=$CXX; export CUDACXX=/usr/local/cuda/bin/nvcc;
-          LIBGOMP=/usr/lib/gcc/x86_64-linux-gnu/10;
+          LIBGCC=/usr/lib/gcc/x86_64-linux-gnu/10;
           /usr/local/bin/cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DHAVE_TESTS=1 -DENABLE_WERROR=1 -DHAVE_AVX2=1 \
-            -DOpenMP_C_FLAGS="-fopenmp -I${LIBGOMP}" -DOpenMP_C_LIB_NAMES=gomp -DOpenMP_CXX_FLAGS="-fopenmp -I${LIBGOMP}" -DOpenMP_CXX_LIB_NAMES=gomp -DOpenMP_gomp_LIBRARY=${LIBGOMP}/libgomp.a \
+            -DOpenMP_C_FLAGS="-fopenmp -I${LIBGCC}" -DOpenMP_C_LIB_NAMES=gomp -DOpenMP_CXX_FLAGS="-fopenmp -I${LIBGCC}" -DOpenMP_CXX_LIB_NAMES=gomp -DOpenMP_gomp_LIBRARY=${LIBGCC}/libgomp.a \
+            -DATOMIC_LIB_OVERRIDE=${LIBGCC}/libatomic.a \
             -DFORCE_STATIC_DEPS=1 -DENABLE_CUDA=1 -DCMAKE_CUDA_ARCHITECTURES="75-real;80-real;86-real;89-real;90" ..
           cmake --build . -j$(nproc --all) -v
           # fail if GLIBC_PRIVATE or too new GLIBC is present
-          readelf -Ws src/mmseqs
-          readelf -V src/mmseqs
           if readelf -Ws src/mmseqs | grep -q GLIBC_PRIVATE; then
+            echo "Error: binary contains private glibc symbols"
             exit 1
           fi
           LIBC_V=$(readelf -V src/mmseqs | awk '$3 ~ /^GLIBC_/ { print $3 }' | sort -V | tail -n1)
           if [[ "$LIBC_V" > "GLIBC_2.29" ]]; then
+            echo "Error: glibc too new"
+            exit 1
+          fi
+          if readelf -d src/mmseqs | grep -q "libatomic.so"; then
+            echo "Error: libatomic.so is present as a dependency"
             exit 1
           fi
         displayName: Build MMseqs2
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c5d4e386..89bc7f31 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -5,6 +5,7 @@ set(HAVE_GPROF 0 CACHE BOOL "Have GPROF Profiler")
 set(ENABLE_WERROR 0 CACHE BOOL "Enable Warnings as Errors")
 #set(DISABLE_LTO 0 CACHE BOOL "Disable link-time optimization in non-debug builds")
 set(REQUIRE_OPENMP 1 CACHE BOOL "Require availability of OpenMP")
+set(ATOMIC_LIB_OVERRIDE "" CACHE PATH "Override path to libatomic")
 
 include(AppendTargetProperty)
 
@@ -117,13 +118,21 @@ if (HAVE_POSIX_MADVISE)
 endif ()
 
 if (NOT DISABLE_IPS4O)
-    find_package(Atomic)
-    if (ATOMIC_FOUND)
-        target_link_libraries(mmseqs-framework ${ATOMIC_LIBRARIES})
+    if (ATOMIC_LIB_OVERRIDE)
+        add_library(LibAtomic STATIC IMPORTED)
+        set_target_properties(LibAtomic PROPERTIES IMPORTED_LOCATION ${ATOMIC_LIB_OVERRIDE})
+        target_link_libraries(mmseqs-framework LibAtomic)
         target_compile_definitions(mmseqs-framework PUBLIC -DENABLE_IPS4O=1)
-        message("-- IPS4O sorting works")
-    else ()
-        message("-- OMPTL sorting fallback")
+        message("-- IPS4O sorting forced with ${ATOMIC_LIB_OVERRIDE}")
+    else()
+        find_package(Atomic)
+        if (ATOMIC_FOUND)
+            target_link_libraries(mmseqs-framework ${ATOMIC_LIBRARIES})
+            target_compile_definitions(mmseqs-framework PUBLIC -DENABLE_IPS4O=1)
+            message("-- IPS4O sorting works")
+        else ()
+            message("-- OMPTL sorting fallback")
+        endif ()
     endif ()
 else ()
     message("-- OMPTL sorting fallback")