diff --git a/pkgs/applications/science/math/caffe/default.nix b/pkgs/applications/science/math/caffe/default.nix
index 08bf84be7c89..462a05d300ce 100644
--- a/pkgs/applications/science/math/caffe/default.nix
+++ b/pkgs/applications/science/math/caffe/default.nix
@@ -91,7 +91,11 @@ stdenv.mkDerivation rec {
     inherit (python.sourceVersion) major minor;  # Should be changed in case of PyPy
   });
 
-  postPatch = lib.optionalString (cudaSupport && lib.versionAtLeast cudatoolkit.version "9.0") ''
+  postPatch = ''
+    substituteInPlace src/caffe/util/io.cpp --replace \
+      'SetTotalBytesLimit(kProtoReadBytesLimit, 536870912)' \
+      'SetTotalBytesLimit(kProtoReadBytesLimit)'
+  '' + lib.optionalString (cudaSupport && lib.versionAtLeast cudatoolkit.version "9.0") ''
     # CUDA 9.0 doesn't support sm_20
     sed -i 's,20 21(20) ,,' cmake/Cuda.cmake
   '';
diff --git a/pkgs/applications/science/math/cntk/default.nix b/pkgs/applications/science/math/cntk/default.nix
index c007490c94d0..ba2225b903fa 100644
--- a/pkgs/applications/science/math/cntk/default.nix
+++ b/pkgs/applications/science/math/cntk/default.nix
@@ -1,4 +1,5 @@
 { lib, stdenv, fetchgit, fetchFromGitHub, cmake
+, fetchpatch
 , openblas, blas, lapack, opencv3, libzip, boost, protobuf, mpi
 , onebitSGDSupport ? false
 , cudaSupport ? false, addOpenGLRunpath, cudatoolkit, nvidia_x11
@@ -28,6 +29,26 @@ in stdenv.mkDerivation rec {
     sha256 = "18l9k7s966a26ywcf7flqyhm61788pcb9fj3wk61jrmgkhy2pcns";
   };
 
+  patches = [
+    # Fix build with protobuf 3.18+
+    # Remove with onnx submodule bump to 1.9+
+    (fetchpatch {
+      url = "https://github.com/onnx/onnx/commit/d3bc82770474761571f950347560d62a35d519d7.patch";
+      extraPrefix = "Source/CNTKv2LibraryDll/proto/onnx/onnx_repo/";
+      stripLen = 1;
+      sha256 = "00raqj8wx30b06ky6cdp5vvc1mrzs7hglyi6h58hchw5lhrwkzxp";
+    })
+  ];
+
+  postPatch = ''
+    # Fix build with protobuf 3.18+
+    substituteInPlace Source/CNTKv2LibraryDll/Serialization.cpp \
+      --replace 'SetTotalBytesLimit(INT_MAX, INT_MAX)' \
+                'SetTotalBytesLimit(INT_MAX)' \
+      --replace 'SetTotalBytesLimit(limit, limit)' \
+                'SetTotalBytesLimit(limit)'
+  '';
+
   nativeBuildInputs = [ cmake ] ++ lib.optional cudaSupport addOpenGLRunpath;
 
   # Force OpenMPI to use g++ in PATH.
diff --git a/pkgs/development/libraries/openvino/default.nix b/pkgs/development/libraries/openvino/default.nix
index b4e487887999..86bc3b0d009c 100644
--- a/pkgs/development/libraries/openvino/default.nix
+++ b/pkgs/development/libraries/openvino/default.nix
@@ -3,6 +3,7 @@
 , autoPatchelfHook
 , stdenv
 , fetchFromGitHub
+, fetchpatch
 , cmake
 , git
 , protobuf
@@ -10,17 +11,29 @@
 , opencv
 , unzip
 , shellcheck
+, srcOnly
 , python
 , enablePython ? false
 }:
 
 let
 
-  onnx_src = fetchFromGitHub {
-    owner = "onnx";
-    repo = "onnx";
-    rev = "v1.8.1";
-    sha256 = "+1zNnZ4lAyVYRptfk0PV7koIX9FqcfD1Ah33qj/G2rA=";
+  onnx_src = srcOnly {
+    name = "onnx-patched";
+    src = fetchFromGitHub {
+      owner = "onnx";
+      repo = "onnx";
+      rev = "v1.8.1";
+      sha256 = "+1zNnZ4lAyVYRptfk0PV7koIX9FqcfD1Ah33qj/G2rA=";
+    };
+    patches = [
+      # Fix build with protobuf 3.18+
+      # Remove with onnx 1.9 release
+      (fetchpatch {
+        url = "https://github.com/onnx/onnx/commit/d3bc82770474761571f950347560d62a35d519d7.patch";
+        sha256 = "0vdsrklkzhdjaj8wdsl4icn93q3961g8dx35zvff0nhpr08wjb7y";
+      })
+    ];
   };
 
 in
diff --git a/pkgs/development/libraries/valhalla/default.nix b/pkgs/development/libraries/valhalla/default.nix
index 6eac19bcb2cd..b3d61e6efd72 100644
--- a/pkgs/development/libraries/valhalla/default.nix
+++ b/pkgs/development/libraries/valhalla/default.nix
@@ -14,6 +14,15 @@ stdenv.mkDerivation rec {
     fetchSubmodules = true;
   };
 
+  # https://github.com/valhalla/valhalla/issues/2119
+  postPatch = ''
+    for f in valhalla/mjolnir/transitpbf.h \
+             src/mjolnir/valhalla_query_transit.cc; do
+      substituteInPlace $f --replace 'SetTotalBytesLimit(limit, limit)' \
+                                     'SetTotalBytesLimit(limit)'
+    done
+  '';
+
   nativeBuildInputs = [ cmake pkg-config ];
   buildInputs = [
     zlib curl protobuf prime-server boost sqlite libspatialite