[Examples] Fix R

It should work now, but it triggers a bug in the IPC subsystem when
exiting, so it can't be added to the CI yet.

Examples/r/Makefile

@@ -27,9 +27,9 @@ LD_LIBRARY_PATH := $(LD_LIBRARY_PATH):$(R_HOME)/lib
 export LD_LIBRARY_PATH
 
 .PHONY: all
-all: R.manifest sh.manifest pal_loader
+all: R.manifest sh.manifest rm.manifest pal_loader
 ifeq ($(SGX),1)
-all: R.manifest.sgx R.sig R.token sh.manifest.sgx sh.sig sh.token
+all: R.manifest.sgx R.sig R.token sh.manifest.sgx sh.sig sh.token rm.manifest.sgx rm.sig rm.token
 endif
 
 include ../../Scripts/Makefile.configs
@@ -85,7 +85,7 @@ R.manifest: R.manifest.template R-trusted-libs
 		-e 's|$$(ARCH_LIBDIR)|'"$(ARCH_LIBDIR)"'|g' \
 		$< > $@
 
-sh.manifest: sh.manifest.template
+%.manifest: %.manifest.template
 	sed -e 's|$$(GRAPHENEDIR)|'"$(GRAPHENEDIR)"'|g' \
 		-e 's|$$(GRAPHENEDEBUG)|'"$(GRAPHENEDEBUG)"'|g' \
 		$< > $@
@@ -94,30 +94,24 @@ sh.manifest: sh.manifest.template
 #   Generating the SGX-specific manifest (R.manifest.sgx), the enclave signature,
 #   and the token for enclave initialization.
 
-R.manifest.sgx: R.manifest sh.manifest.sgx
+%.manifest.sgx: %.manifest
 	$(GRAPHENEDIR)/Pal/src/host/Linux-SGX/signer/pal-sgx-sign \
 		-libpal $(GRAPHENEDIR)/Runtime/libpal-Linux-SGX.so \
 		-key $(SGX_SIGNER_KEY) \
 		-manifest $< -output $@
 
+# Theoretically we could write "%.sig: %.manifest.sgx" or use a "Rule with Grouped Targets"
+# ("%.manifest.sgx %.sig &: %.manifest") but neither of this works (Make is broken?).
 R.sig: R.manifest.sgx
-
-R.token: R.sig
-	$(GRAPHENEDIR)/Pal/src/host/Linux-SGX/signer/pal-sgx-get-token \
-		-output R.token -sig R.sig
-
-# sh.manifest.sgx is needed for R to run the shell for file clean-up
-sh.manifest.sgx: sh.manifest
-	$(GRAPHENEDIR)/Pal/src/host/Linux-SGX/signer/pal-sgx-sign \
-		-libpal $(GRAPHENEDIR)/Runtime/libpal-Linux-SGX.so \
-		-key $(SGX_SIGNER_KEY) \
-		-manifest $< -output $@
-
 sh.sig: sh.manifest.sgx
+rm.sig: rm.manifest.sgx
 
-sh.token: sh.sig
-	$(GRAPHENEDIR)/Pal/src/host/Linux-SGX/signer/pal-sgx-get-token \
-		-output sh.token -sig sh.sig
+%.token: %.sig
+	$(GRAPHENEDIR)/Pal/src/host/Linux-SGX/signer/pal-sgx-get-token -output $@ -sig $<
+
+# sh and rm are used by R for file clean-up
+R.manifest.sgx: sh.sig
+sh.manifest.sgx: rm.sig
 
 # Extra executables
 pal_loader:
@@ -126,3 +120,6 @@ pal_loader:
 .PHONY: clean
 clean:
 	$(RM) *.manifest *.manifest.sgx *.token *.sig pal_loader
+
+.PHONY: distclean
+distclean: clean

Examples/r/R.manifest.template

@@ -56,6 +56,10 @@ fs.mount.tmp.type = chroot
 fs.mount.tmp.path = /tmp
 fs.mount.tmp.uri = file:/tmp
 
+# Mount host's /bin
+fs.mount.bin.type = chroot
+fs.mount.bin.path = /bin
+fs.mount.bin.uri = file:/bin
 
 # SGX general options
 
@@ -93,7 +97,9 @@ sgx.allowed_files.tmp = file:/tmp
 sgx.allowed_files.r_etc = file:$(R_HOME)/etc
 sgx.allowed_files.r_lib = file:$(R_HOME)/library
 
-# Allow creating child enclaves for sh
+# R uses shell to delete files, so we need to allow /bin/sh and /bin/rm to be spawned.
+# strace snippet: execve("/bin/sh", ["sh", "-c", "rm -rf /tmp/RtmpEiedDF"], [/* 41 vars */])
+
 sgx.trusted_files.sh = file:/bin/sh
 sgx.trusted_children.sh = file:sh.sig
 

Examples/r/rm.manifest.template

@@ -0,0 +1,32 @@
+# rm manifest example
+#
+# This manifest was prepared and tested on Ubuntu 16.04.
+
+loader.exec = file:/bin/rm
+loader.preload = file:$(GRAPHENEDIR)/Runtime/libsysdb.so
+loader.debug_type = $(GRAPHENEDEBUG)
+
+# Don't use this on production!
+loader.insecure__use_cmdline_argv = 1
+
+loader.env.LD_LIBRARY_PATH = /lib
+
+fs.mount.lib.type = chroot
+fs.mount.lib.path = /lib
+fs.mount.lib.uri = file:$(GRAPHENEDIR)/Runtime
+
+fs.mount.tmp.type = chroot
+fs.mount.tmp.path = /tmp
+fs.mount.tmp.uri = file:/tmp
+
+fs.mount.bin.type = chroot
+fs.mount.bin.path = /bin
+fs.mount.bin.uri = file:/bin
+
+sgx.enclave_size = 1G
+sgx.thread_num = 4
+
+sgx.trusted_files.ld = file:$(GRAPHENEDIR)/Runtime/ld-linux-x86-64.so.2
+sgx.trusted_files.libc = file:$(GRAPHENEDIR)/Runtime/libc.so.6
+
+sgx.zero_heap_on_demand = 1

Examples/r/sh.manifest.template

@@ -24,12 +24,22 @@ fs.mount.lib.type = chroot
 fs.mount.lib.path = /lib
 fs.mount.lib.uri = file:$(GRAPHENEDIR)/Runtime
 
+# Mount /tmp
+fs.mount.tmp.type = chroot
+fs.mount.tmp.path = /tmp
+fs.mount.tmp.uri = file:/tmp
+
+# Mount host's /bin
+fs.mount.bin.type = chroot
+fs.mount.bin.path = /bin
+fs.mount.bin.uri = file:/bin
+
 # SGX general options
 
 # Set the virtual memory size of the SGX enclave. For SGX v1, the enclave size
 # must be specified during signing. If sh needs more virtual memory than the
 # enclave size, Graphene will not be able to allocate it.
-sgx.enclave_size = 256M
+sgx.enclave_size = 1G
 
 # Set the maximum number of enclave threads. For SGX v1, the number of enclave
 # TCSes must be specified during signing, so the application cannot use more
@@ -37,10 +47,13 @@ sgx.enclave_size = 256M
 # thread for handling inter-process communication (IPC), and potentially another
 # thread for asynchronous events. Therefore, the actual number of threads that
 # the application can create is (sgx.thread_num - 2).
-sgx.thread_num = 2
+sgx.thread_num = 4
 
 # SGX trusted libraries
 sgx.trusted_files.ld = file:$(GRAPHENEDIR)/Runtime/ld-linux-x86-64.so.2
 sgx.trusted_files.libc = file:$(GRAPHENEDIR)/Runtime/libc.so.6
 
+sgx.trusted_files.rm = file:/bin/rm
+sgx.trusted_children.rm = file:rm.sig
+
 sgx.zero_heap_on_demand = 1